Pubvar

12:103232934:C/A

GRCh37/hg19 position	12:103232934
GRCh38/hg38 position	12:102839156
Alleles (ref/alt)	C/A
dbSNP rsid	rs372637021
Gene symbol	PAH
Most severe consequence	3_prime_UTR_variant
Flanking sequence	GATCTCCATCAACAGATTCACAGCTGACAGA[C/A]CACATTCTGTCCATGGCTTTACTTTATTTTC
HGVS	NM_000277.3:c.19G>T NM_001354304.2:c.19G>T

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Gene annotations

Transcript	Gene	Exon number	Consequence	HGVS cDNA	HGVS protein	Location	Protein location
NM_000277.3	PAH	13	3_prime_UTR_variant	c.*19G>T	-	3' UTR
NM_001354304.2	PAH	14	3_prime_UTR_variant	c.*19G>T	-	3' UTR

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Population frequency

Select populations: ALL LWK MKK YRI EUR FIN NFE CEU ASJ TSI EAS SAS CHB HAN CHD JPT AFR AMR ASW GIH MEX OTH

Database	Population	AC	AN	Hom	AF
1000 genomes	ALL	13	5008	-	0.00259585
	EUR	-	-	-	0.002
	EAS	-	-	-	0.001
	SAS	-	-	-	0.0102
	AFR	-	-	-	0
	AMR	-	-	-	0
ExAC	ALL	261	120776	5	0.002161
	FIN	1	6600	0	0.000152
	NFE	84	66444	1	0.001264
	EAS	22	8606	0	0.002556
	SAS	129	16472	3	0.007831
	AFR	2	10310	0	0.000194
	AMR	20	11438	1	0.001749
	OTH	3	906	0	0.003311
gnomAD genomes	ALL	25	30978	0	0.000807024
	FIN	0	3494	0	0
	NFE	16	15010	0	0.00106596
	ASJ	0	302	0	0
	EAS	3	1618	0	0.00185414
	AFR	5	8734	0	0.000572475
	AMR	1	838	0	0.00119332
	OTH	0	982	0	0
gnomAD exomes	ALL	539	245694	8	0.00219379
	FIN	2	22252	0	8.98796e-05
	NFE	159	111330	2	0.00142819
	ASJ	9	9842	0	0.000914448
	EAS	42	17240	0	0.00243619
	SAS	250	30776	4	0.00812321
	AFR	1	15282	0	6.54365e-05
	AMR	62	33502	2	0.00185064
	OTH	14	5470	0	0.00255941
CONVERGE	ALL	-	-	-	0.002
HRC	ALL	82	64976	-	0.001262

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View on UCSC genome browser

Conservation

Conservation scores are retrieved from UCSC genome browser. The conservation levels are defined by simple cutoff values. If the conservation levels do not agree with each other, you can manually check whether this variant is conserved with UCSC genome browser.

Method	Score	Level
GERP++	-2.17	Not conserved
phastCons46way primates	0.035	Not conserved
phastCons46way placental	0.000	Not conserved
phastCons100way vertebrates	0.000	Not conserved
phyloP46way primates	-0.490	Not conserved
phyloP46way placental	-0.406	Not conserved
phyloP100way vertebrates	-0.788	Not conserved

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ClinVar

Accession	Clinical significance	Date last evaluated	Review status	Method	Disease name	Disease symbol	Disease inheritance	Pubmed
RCV000252084	Likely benign	2023-01-25	criteria provided, multiple submitters, no conflicts	clinical testing	not specified	-	-	26210745 35339094 12765842 26467025 25741868
RCV000538868	Uncertain significance	2019-09-27	reviewed by expert panel	clinical testing	Phenylketonuria	PKU	Autosomal recessive inheritance	26210745 12765842 25741868 28492532

Accession

Clinical significance

Date last evaluated

Review status

Method

Disease name

Disease symbol

Disease inheritance

Pubmed

RCV000252084

Likely benign

2023-01-25

criteria provided, multiple submitters, no conflicts

clinical testing

not specified

Uncertain significance

2019-09-27

reviewed by expert panel

clinical testing

Phenylketonuria

PKU

Autosomal recessive inheritance

InterVar

InterVar is a software tool for clinical interpretation of genetic variants by the ACMG/AMP 2015 guideline. The eveidence tags that variant met are highlighted. Please note that evidence tags with need to be evaluated manually.

Class: Uncertain significance

	Benign		Pathogenic
	Strong	Supporting	Supporting	Moderate	Strong	Very Strong
Population data	BA1 BS1 BS2			PM2	PS4
Computational and predictive data		BP1 BP3 BP4 BP7	PP3	PM4 PM5	PS1	PVS1
Functional data	BS3		PP2	PM1	PS3
Segregation data	BS4		PP1	PP1	PP1
De novo data				PM6	PS2
Allelic data		BP2		PM3
Other database		BP6	PP5
Other data		BP5	PP4