dbSNP rs3803107: AVPR1A:c.*305C>T (chr12-63147054-G-A) – 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.*305C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 273,904 control chromosomes in the GnomAD database, including 5,980 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 0.21 ( 4097 hom., cov: 33)

Exomes 𝑓: 0.16 ( 1883 hom. )

Consequence

AVPR1A
NM_000706.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.593

Publications

22 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000706.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AVPR1A	NM_000706.5	MANE Select	c.*305C>T		3_prime_UTR	Exon 2 of 2	NP_000697.1	P37288

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AVPR1A	ENST00000299178.4	TSL:1 MANE Select	c.*305C>T		3_prime_UTR	Exon 2 of 2	ENSP00000299178.3	P37288
	AVPR1A	ENST00000550940.1	TSL:3	c.538+367C>T		intron	N/A	ENSP00000449822.1	F8VW98

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32215

AN:

151950

Hom.:

4094

Cov.:

show subpopulations

Gnomad AFR

AF:

0.348

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.191

GnomAD4 exome

AF:

0.164

AC:

19969

AN:

121836

Hom.:

1883

Cov.:

AF XY:

0.165

AC XY:

10245

AN XY:

62268

show subpopulations

African (AFR)

AF:

0.342

AC:

1594

AN:

4664

American (AMR)

AF:

0.102

AC:

616

AN:

6048

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

765

AN:

4394

East Asian (EAS)

AF:

0.145

AC:

1453

AN:

10030

South Asian (SAS)

AF:

0.285

AC:

1578

AN:

5528

European-Finnish (FIN)

AF:

0.117

AC:

668

AN:

5696

Middle Eastern (MID)

AF:

0.191

AC:

AN:

508

European-Non Finnish (NFE)

AF:

0.154

AC:

11894

AN:

77298

Other (OTH)

AF:

0.170

AC:

1304

AN:

7670

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

809

1619

2428

3238

4047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

134

268

402

536

670

<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:

0.212

AC:

32239

AN:

152068

Hom.:

4097

Cov.:

AF XY:

0.209

AC XY:

15576

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.347

AC:

14399

AN:

41450

American (AMR)

AF:

0.144

AC:

2198

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.190

AC:

659

AN:

3470

East Asian (EAS)

AF:

0.149

AC:

771

AN:

5174

South Asian (SAS)

AF:

0.321

AC:

1548

AN:

4822

European-Finnish (FIN)

AF:

0.109

AC:

1151

AN:

10576

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.159

AC:

10823

AN:

67976

Other (OTH)

AF:

0.189

AC:

400

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1232

2464

3695

4927

6159

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<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:

0.169

Hom.:

3625

Bravo

AF:

0.215

Asia WGS

AF:

0.254

AC:

886

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.47

(source)

DANN

Benign

0.61

PhyloP100

-0.59

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over