1-206112629-G-T

Variant summary

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

The NM_000707.5(AVPR1B):c.941-2106C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0413 in 152,182 control chromosomes in the GnomAD database, including 184 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 0.041 (184 hom., cov: 32)
• Consequence: AVPR1B NM_000707.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AVPR1B	NM_000707.5	c.941-2106C>A		intron_variant		ENST00000367126.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AVPR1B	ENST00000367126.5	c.941-2106C>A		intron_variant		1	NM_000707.5	P1
AVPR1B	ENST00000612906.1	n.37-2106C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0413 AC: 6282 AN: 152064 Hom.: 184 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00790

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0639

Gnomad OTH AF: 0.0508

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

GnomAD4 genome AF: 0.0413 AC: 6281 AN: 152182 Hom.: 184 Cov.: 32 AF XY: 0.0390 AC XY: 2898 AN XY: 74388

Gnomad4 AFR AF: 0.0116

Gnomad4 AMR AF: 0.0417

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00811

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0639

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0555 Hom.: 216

Bravo AF: 0.0403

Asia WGS AF: 0.00635 AC: 23 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	4.5
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35810727; hg19: chr1-206228702;