Pubvar

12:103232809:T/C

GRCh37/hg19 position	12:103232809
GRCh38/hg38 position	12:102839031
Alleles (ref/alt)	T/C
dbSNP rsid	rs375319584
Gene symbol	PAH
Most severe consequence	3_prime_UTR_variant
Flanking sequence	CTCATATCCTGTCATTTCAGATTATTTTGAC[T/C]TATTTGTTGTTTCTCCATCTTGTAAAGGATT
HGVS	NM_000277.3:c.144A>G NM_001354304.2:c.144A>G

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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.*144A>G	-	3' UTR
NM_001354304.2	PAH	14	3_prime_UTR_variant	c.*144A>G	-	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	17	5008	-	0.00339457
	EUR	-	-	-	0
	EAS	-	-	-	0.001
	SAS	-	-	-	0.0164
	AFR	-	-	-	0
	AMR	-	-	-	0
gnomAD genomes	ALL	4	30972	0	0.000129149
	FIN	0	3494	0	0
	NFE	0	15004	0	0
	ASJ	0	302	0	0
	EAS	2	1618	0	0.00123609
	AFR	1	8734	0	0.000114495
	AMR	0	838	0	0
	OTH	1	982	0	0.00101833
CONVERGE	ALL	-	-	-	0.002
HRC	ALL	17	64976	-	0.000261635

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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++	2.3	Conserved
phastCons46way primates	0.002	Not conserved
phastCons46way placental	0.002	Not conserved
phastCons100way vertebrates	0.643	Conserved
phyloP46way primates	-0.399	Not conserved
phyloP46way placental	0.384	Not conserved
phyloP100way vertebrates	0.279	Not conserved

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ClinVar

Accession	Clinical significance	Date last evaluated	Review status	Method	Disease name	Disease symbol	Disease inheritance	Pubmed
RCV000814338	Uncertain significance	2020-12-23	reviewed by expert panel	curation	Phenylketonuria	PKU	Autosomal recessive inheritance	24130151 20188615 28492532

Accession

Clinical significance

Date last evaluated

Review status

Method

Disease name

Disease symbol

Disease inheritance

Pubmed

RCV000814338

Uncertain significance

2020-12-23

reviewed by expert panel

curation

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