rs11174811

Positions:

• chr12-63146696-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000706.5(AVPR1A):​c.*663G>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 0.121 in 152,200 control chromosomes in the GnomAD database, including 1,231 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 0.12 (1231 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: AVPR1A NM_000706.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AVPR1A	NM_000706.5	c.*663G>T		3_prime_UTR_variant	2/2	ENST00000299178.4	NP_000697.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AVPR1A	ENST00000299178.4	c.*663G>T		3_prime_UTR_variant	2/2	1	NM_000706.5	ENSP00000299178	P1
AVPR1A	ENST00000550940.1	c.538+725G>T		intron_variant		3		ENSP00000449822

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18477 AN: 152080 Hom.: 1230 Cov.: 33

Gnomad AFR AF: 0.0929

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.117

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.121 AC: 18491 AN: 152200 Hom.: 1231 Cov.: 33 AF XY: 0.120 AC XY: 8920 AN XY: 74410

Gnomad4 AFR AF: 0.0928

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0943

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.116

Alfa AF: 0.139 Hom.: 1741

Bravo AF: 0.117

Asia WGS AF: 0.0970 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.36

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

LitVar

Other links and lift over

dbSNP: rs11174811; hg19: chr12-63540476;