chr1-206108533-T-A

Position:

• chr1-206108533-T-A

Variant summary

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

The NM_000707.5(AVPR1B):​c.*1656A>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 0.181 in 152,220 control chromosomes in the GnomAD database, including 2,741 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 0.18 (2741 hom., cov: 32)
• Consequence: AVPR1B NM_000707.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AVPR1B	NM_000707.5	c.*1656A>T		3_prime_UTR_variant	2/2	ENST00000367126.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AVPR1B	ENST00000367126.5	c.*1656A>T		3_prime_UTR_variant	2/2	1	NM_000707.5	P1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27448 AN: 152104 Hom.: 2731 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.186

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.181 AC: 27490 AN: 152220 Hom.: 2741 Cov.: 32 AF XY: 0.181 AC XY: 13484 AN XY: 74430

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.184

Alfa AF: 0.159 Hom.: 301

Bravo AF: 0.184

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28418396; hg19: chr1-206232798;