rs28536160

Variant names:

• chr1-206117948-A-G
• rs28536160
• ENST00000425896.1:n.44-122A>G

Variant summary

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

The ENST00000425896.1(AVPR1B-DT):​n.44-122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,182 control chromosomes in the GnomAD database, including 5,397 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 (5396 hom., cov: 31)
  • Exomes 𝑓: 0.071 (1 hom.)
• Consequence: AVPR1B-DT ENST00000425896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

Genes affected

AVPR1B-DT (HGNC:55832): (AVPR1B divergent transcript)

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 = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AVPR1B-DT	NR_186693.1	n.44-122A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AVPR1B-DT	ENST00000425896.1	n.44-122A>G		intron_variant	Intron 1 of 2	3
AVPR1B	ENST00000612906.1	n.-249T>C		upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27001 AN: 151924 Hom.: 5375 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0839

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.0555

Gnomad FIN AF: 0.0681

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.149

GnomAD4 exome AF: 0.0714 AC: 10 AN: 140 Hom.: 1 Cov.: 0 AF XY: 0.0581 AC XY: 5 AN XY: 86

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0833

Gnomad4 NFE exome AF: 0.0395

Gnomad4 OTH exome AF: 0.0500

GnomAD4 genome AF: 0.178 AC: 27064 AN: 152042 Hom.: 5396 Cov.: 31 AF XY: 0.173 AC XY: 12855 AN XY: 74340

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.0838

Gnomad4 ASJ AF: 0.0982

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.0551

Gnomad4 FIN AF: 0.0681

Gnomad4 NFE AF: 0.0481

Gnomad4 OTH AF: 0.147

Alfa AF: 0.185 Hom.: 1026

Bravo AF: 0.195

Asia WGS AF: 0.0610 AC: 214 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	7.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28536160; hg19: chr1-206223383;