dbSNP rs35608965: AVPR1B:c.-29T>C (chr1-206116919-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000707.5(AVPR1B):c.-29T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 1,574,190 control chromosomes in the GnomAD database, including 2,073 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 0.061 ( 353 hom., cov: 32)

Exomes 𝑓: 0.044 ( 1720 hom. )

Consequence

AVPR1B
NM_000707.5 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0600

Variant links:

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]

AVPR1B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 = 0.0968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AVPR1B	NM_000707.5 link	c.-29T>C		5_prime_UTR_variant	Exon 1 of 2	ENST00000367126.5	NP_000698.1	P47901

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AVPR1B	ENST00000367126.5 link	c.-29T>C		5_prime_UTR_variant	Exon 1 of 2	1	NM_000707.5	ENSP00000356094.4		P47901
AVPR1B	ENST00000612906.1 link	n.36+745T>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes

AF:

0.0611

AC:

9289

AN:

152020

Hom.:

353

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0991

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0377

Gnomad ASJ

AF:

0.0919

Gnomad EAS

AF:

0.00617

Gnomad SAS

AF:

0.0475

Gnomad FIN

AF:

0.0680

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0461

Gnomad OTH

AF:

0.0590

GnomAD3 exomes

AF:

0.0490

AC:

10979

AN:

224204

Hom.:

362

AF XY:

0.0493

AC XY:

5951

AN XY:

120774

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.0263

Gnomad ASJ exome

AF:

0.0950

Gnomad EAS exome

AF:

0.00565

Gnomad SAS exome

AF:

0.0494

Gnomad FIN exome

AF:

0.0604

Gnomad NFE exome

AF:

0.0497

Gnomad OTH exome

AF:

0.0575

GnomAD4 exome

AF:

0.0440

AC:

62594

AN:

1422052

Hom.:

1720

Cov.:

AF XY:

0.0446

AC XY:

31394

AN XY:

704664

show subpopulations

Gnomad4 AFR exome

AF:

0.109

Gnomad4 AMR exome

AF:

0.0288

Gnomad4 ASJ exome

AF:

0.0951

Gnomad4 EAS exome

AF:

0.00747

Gnomad4 SAS exome

AF:

0.0515

Gnomad4 FIN exome

AF:

0.0601

Gnomad4 NFE exome

AF:

0.0408

Gnomad4 OTH exome

AF:

0.0508

GnomAD4 genome

AF:

0.0611

AC:

9302

AN:

152138

Hom.:

353

Cov.:

AF XY:

0.0608

AC XY:

4522

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.0993

Gnomad4 AMR

AF:

0.0376

Gnomad4 ASJ

AF:

0.0919

Gnomad4 EAS

AF:

0.00619

Gnomad4 SAS

AF:

0.0474

Gnomad4 FIN

AF:

0.0680

Gnomad4 NFE

AF:

0.0461

Gnomad4 OTH

AF:

0.0575

Alfa

AF:

0.0588

Hom.:

Bravo

AF:

0.0606

Asia WGS

AF:

0.0270

AC:

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

5.9

DANN

Benign

0.66

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over