rs3803107

Variant names:

• chr12-63147054-G-A
• rs3803107
• NM_000706.5:c.*305C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

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

ACMG classification

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

Selected	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

Ensembl Transcripts

Selected	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
	AVPR1A	ENST00000550940.1	TSL:3	c.538+367C>T		intron	N/A	ENSP00000449822.1

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

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: 97 AN: 508

European-Non Finnish (NFE) AF: 0.154 AC: 11894 AN: 77298

Other (OTH) AF: 0.170 AC: 1304 AN: 7670

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

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: 54 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10823 AN: 67976

Other (OTH) AF: 0.189 AC: 400 AN: 2116

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
DANN	Benign	0.61
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3803107; hg19: chr12-63540834;