rs3803107

Positions:

• chr12-63147054-G-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AVPR1A	NM_000706.5	c.*305C>T		3_prime_UTR_variant	2/2	ENST00000299178.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AVPR1A	ENST00000299178.4	c.*305C>T		3_prime_UTR_variant	2/2	1	NM_000706.5	P1
AVPR1A	ENST00000550940.1	c.538+367C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32215 AN: 151950 Hom.: 4094 Cov.: 33

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.: 3 AF XY: 0.165 AC XY: 10245 AN XY: 62268

Gnomad4 AFR exome AF: 0.342

Gnomad4 AMR exome AF: 0.102

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.145

Gnomad4 SAS exome AF: 0.285

Gnomad4 FIN exome AF: 0.117

Gnomad4 NFE exome AF: 0.154

Gnomad4 OTH exome AF: 0.170

GnomAD4 genome AF: 0.212 AC: 32239 AN: 152068 Hom.: 4097 Cov.: 33 AF XY: 0.209 AC XY: 15576 AN XY: 74350

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.189

Alfa AF: 0.168 Hom.: 3023

Bravo AF: 0.215

Asia WGS AF: 0.254 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.61

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: rs3803107; hg19: chr12-63540834;