Genetic Variant AVPR1A:c.*2493C>G (chr12-63144866-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000706.5(AVPR1A):c.*2493C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,810 control chromosomes in the GnomAD database, including 8,035 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 8028 hom., cov: 32)

Exomes 𝑓: 0.13 ( 7 hom. )

Consequence

AVPR1A
NM_000706.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.556

Publications

11 publications found

Variant links:

Genes affected

AVPR1A (HGNC:895): (arginine vasopressin receptor 1A) The protein encoded by this gene acts as receptor for arginine vasopressin. This receptor belongs to the subfamily of G-protein coupled receptors which includes AVPR1B, V2R and OXT receptors. Its activity is mediated by G proteins which stimulate a phosphatidylinositol-calcium second messenger system. The receptor mediates cell contraction and proliferation, platelet aggregation, release of coagulation factor and glycogenolysis. [provided by RefSeq, Jul 2008]

AVPR1A Gene-Disease associations (from GenCC):

autism spectrum disorder
Inheritance: Unknown Classification: NO_KNOWN Submitted by: ClinGen

AVPR1A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AVPR1A	NM_000706.5 link	c.*2493C>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000299178.4	NP_000697.1	P37288X5D2B0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AVPR1A	ENST00000299178.4 link	c.*2493C>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_000706.5	ENSP00000299178.3		P37288

Frequencies

GnomAD3 genomes

AF:

0.278

AC:

42193

AN:

151932

Hom.:

8006

Cov.:

show subpopulations

Gnomad AFR

AF:

0.539

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.327

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.250

GnomAD4 exome

AF:

0.134

AC:

102

AN:

760

Hom.:

Cov.:

AF XY:

0.158

AC XY:

AN XY:

400

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.0952

AC:

AN:

126

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.111

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.137

AC:

AN:

554

Other (OTH)

AF:

0.154

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.278

AC:

42252

AN:

152050

Hom.:

8028

Cov.:

AF XY:

0.274

AC XY:

20354

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.539

AC:

22355

AN:

41456

American (AMR)

AF:

0.175

AC:

2675

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

734

AN:

3470

East Asian (EAS)

AF:

0.149

AC:

769

AN:

5172

South Asian (SAS)

AF:

0.326

AC:

1574

AN:

4822

European-Finnish (FIN)

AF:

0.147

AC:

1560

AN:

10582

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.173

AC:

11756

AN:

67966

Other (OTH)

AF:

0.247

AC:

520

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1356

2711

4067

5422

6778

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

408

816

1224

1632

2040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.120

Hom.:

248

Bravo

AF:

0.284

Asia WGS

AF:

0.274

AC:

956

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.56

(source)

DANN

Benign

0.58

PhyloP100

-0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over