NM_000707.5:c.941-2106C>A

Variant names:

• chr1-206112629-G-T
• rs35810727
• NM_000707.5:c.941-2106C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AVPR1B	NM_000707.5	c.941-2106C>A		intron_variant	Intron 1 of 1	ENST00000367126.5	NP_000698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AVPR1B	ENST00000367126.5	c.941-2106C>A		intron_variant	Intron 1 of 1	1	NM_000707.5	ENSP00000356094.4
AVPR1B	ENST00000612906.1	n.37-2106C>A		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.0116 AC: 483 AN: 41532

American (AMR) AF: 0.0417 AC: 638 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00811 AC: 39 AN: 4806

European-Finnish (FIN) AF: 0.0436 AC: 462 AN: 10600

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0639 AC: 4346 AN: 67998

Other (OTH) AF: 0.0498 AC: 105 AN: 2110

Alfa AF: 0.0548 Hom.: 388

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs35810727; hg19: chr1-206228702;