rs33985287

chr1-206110072-T-C

Variant summary

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

The NM_000707.5(AVPR1B):c.*117A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 1,246,046 control chromosomes in the GnomAD database, including 25,395 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 0.27 (7634 hom., cov: 32)
  • Exomes 𝑓: 0.17 (17761 hom.)
• Consequence: AVPR1B NM_000707.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

AVPR1B (HGNC:896): (arginine vasopressin receptor 1B) 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 AVPR1A, V2R and OXT receptors. Its activity is mediated by G proteins which stimulate a phosphatidylinositol-calcium second messenger system. The receptor is primarily located in the anterior pituitary, where it stimulates ACTH release. It is expressed at high levels in ACTH-secreting pituitary adenomas as well as in bronchial carcinoids responsible for the ectopic ACTH syndrome. A spliced antisense transcript of this gene has been reported but its function is not known. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AVPR1B	NM_000707.5	c.*117A>G		3_prime_UTR_variant	2/2	ENST00000367126.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AVPR1B	ENST00000367126.5	c.*117A>G		3_prime_UTR_variant	2/2	1	NM_000707.5	P1
AVPR1B	ENST00000612906.1	n.488A>G		non_coding_transcript_exon_variant	2/2	4

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40574 AN: 151900 Hom.: 7619 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.254

GnomAD4 exome AF: 0.166 AC: 181333 AN: 1094028 Hom.: 17761 Cov.: 16 AF XY: 0.168 AC XY: 90415 AN XY: 537760

Gnomad4 AFR exome AF: 0.547

Gnomad4 AMR exome AF: 0.170

Gnomad4 ASJ exome AF: 0.222

Gnomad4 EAS exome AF: 0.127

Gnomad4 SAS exome AF: 0.255

Gnomad4 FIN exome AF: 0.161

Gnomad4 NFE exome AF: 0.148

Gnomad4 OTH exome AF: 0.185

GnomAD4 genome AF: 0.267 AC: 40636 AN: 152018 Hom.: 7634 Cov.: 32 AF XY: 0.265 AC XY: 19667 AN XY: 74312

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.250

Alfa AF: 0.175 Hom.: 4268

Bravo AF: 0.281

Asia WGS AF: 0.208 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.6
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs33985287; hg19: chr1-206231259;