rs3741865

Positions:

• chr12-63151078-G-A
• chr12-63151078-G-C
• chr12-63151078-G-T

Variant summary

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

The NM_000706.5(AVPR1A):​c.-242C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0211 in 517,080 control chromosomes in the GnomAD database, including 594 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 0.016 (105 hom., cov: 32)
  • Exomes 𝑓: 0.023 (489 hom.)
• Consequence: AVPR1A NM_000706.5 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

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]

ENSG00000279444 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AVPR1A	NM_000706.5	c.-242C>T		5_prime_UTR_premature_start_codon_gain_variant	1/2	ENST00000299178.4	NP_000697.1
AVPR1A	NM_000706.5	c.-242C>T		5_prime_UTR_variant	1/2	ENST00000299178.4	NP_000697.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AVPR1A	ENST00000299178.4	c.-242C>T		5_prime_UTR_premature_start_codon_gain_variant	1/2	1	NM_000706.5	ENSP00000299178.3
AVPR1A	ENST00000299178.4	c.-242C>T		5_prime_UTR_variant	1/2	1	NM_000706.5	ENSP00000299178.3
ENSG00000279444	ENST00000624438.1	n.14G>A		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes AF: 0.0159 AC: 2409 AN: 151968 Hom.: 105 Cov.: 32

Gnomad AFR AF: 0.0100

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.00249

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.00666

Gnomad OTH AF: 0.0105

GnomAD4 exome AF: 0.0233 AC: 8519 AN: 364994 Hom.: 489 Cov.: 5 AF XY: 0.0267 AC XY: 4991 AN XY: 187242

Gnomad4 AFR exome AF: 0.00853

Gnomad4 AMR exome AF: 0.00279

Gnomad4 ASJ exome AF: 0.00292

Gnomad4 EAS exome AF: 0.123

Gnomad4 SAS exome AF: 0.126

Gnomad4 FIN exome AF: 0.0163

Gnomad4 NFE exome AF: 0.00598

Gnomad4 OTH exome AF: 0.0184

GnomAD4 genome AF: 0.0158 AC: 2402 AN: 152086 Hom.: 105 Cov.: 32 AF XY: 0.0185 AC XY: 1373 AN XY: 74340

Gnomad4 AFR AF: 0.0100

Gnomad4 AMR AF: 0.00248

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0141

Gnomad4 NFE AF: 0.00666

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.00632 Hom.: 3

Bravo AF: 0.0120

Asia WGS AF: 0.135 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3741865; hg19: chr12-63544858;