rs28418396

Variant names:

• chr1-206108533-T-A
• rs28418396
• NM_000707.5:c.*1656A>T

Variant summary

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000707.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AVPR1B	NM_000707.5	MANE Select	c.*1656A>T		3_prime_UTR	Exon 2 of 2	NP_000698.1	P47901

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AVPR1B	ENST00000367126.5	TSL:1 MANE Select	c.*1656A>T		3_prime_UTR	Exon 2 of 2	ENSP00000356094.4	P47901

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

African (AFR) AF: 0.254 AC: 10557 AN: 41514

American (AMR) AF: 0.166 AC: 2531 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3472

East Asian (EAS) AF: 0.103 AC: 533 AN: 5192

South Asian (SAS) AF: 0.253 AC: 1220 AN: 4826

European-Finnish (FIN) AF: 0.143 AC: 1517 AN: 10600

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9913 AN: 68006

Other (OTH) AF: 0.184 AC: 388 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.79
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs28418396; hg19: chr1-206232798;