Pubvar

12:103232766:C/T

GRCh37/hg19 position	12:103232766
GRCh38/hg38 position	12:102838988
Alleles (ref/alt)	C/T
dbSNP rsid	rs1801153
Gene symbol	PAH
Most severe consequence	3_prime_UTR_variant
Flanking sequence	AAGATGACCCCAAAAGATTTACCATTATGCT[C/T]TTGAGTATGTACTCATATCCTGTCATTTCAG
HGVS	NM_000277.3:c.187G>A NM_001354304.2:c.187G>A

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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.*187G>A	-	3' UTR
NM_001354304.2	PAH	14	3_prime_UTR_variant	c.*187G>A	-	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	1465	5008	-	0.292532
	EUR	-	-	-	0.2078
	EAS	-	-	-	0.006
	SAS	-	-	-	0.1411
	AFR	-	-	-	0.6415
	AMR	-	-	-	0.3804
gnomAD genomes	ALL	9340	30892	1952	0.302344
	FIN	659	3490	59	0.188825
	NFE	3030	14976	322	0.202324
	ASJ	54	302	6	0.178808
	EAS	10	1614	0	0.00619579
	AFR	5048	8704	1475	0.579963
	AMR	327	834	70	0.392086
	OTH	212	972	20	0.218107
CONVERGE	ALL	-	-	-	0.007
HRC	ALL	13338	64976	-	0.205276

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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++	1.66	Not conserved
phastCons46way primates	0.004	Not conserved
phastCons46way placental	0.002	Not conserved
phastCons100way vertebrates	0.068	Not conserved
phyloP46way primates	-0.352	Not conserved
phyloP46way placental	0.272	Not conserved
phyloP100way vertebrates	0.622	Not conserved

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ClinVar

Accession	Clinical significance	Date last evaluated	Review status	Method	Disease name	Disease symbol	Disease inheritance	Pubmed
RCV001618535	Benign	2018-09-22	criteria provided, single submitter	clinical testing	not provided	-	-	-
RCV000289289	Benign	2018-01-13	criteria provided, single submitter	clinical testing	Phenylketonuria	PKU	-	-

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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: Benign

	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