1-206110067-C-T

Variant names:

• chr1-206110067-C-T
• rs33933482
• ENST00000367126:c.*122G>A

Variant summary

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

The NM_000707.5(AVPR1B):​c.*122G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 1,208,700 control chromosomes in the GnomAD database, including 15,430 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 0.21 (4626 hom., cov: 32)
  • Exomes 𝑓: 0.13 (10804 hom.)
• Consequence: AVPR1B NM_000707.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AVPR1B	NM_000707.5	c.*122G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000367126.5	NP_000698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AVPR1B	ENST00000367126	c.*122G>A		3_prime_UTR_variant	Exon 2 of 2	1	NM_000707.5	ENSP00000356094.4
AVPR1B	ENST00000612906.1	n.493G>A		non_coding_transcript_exon_variant	Exon 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31316 AN: 151930 Hom.: 4621 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.195

GnomAD4 exome AF: 0.132 AC: 138996 AN: 1056652 Hom.: 10804 Cov.: 15 AF XY: 0.134 AC XY: 69517 AN XY: 518992

Gnomad4 AFR exome AF: 0.424

Gnomad4 AMR exome AF: 0.136

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.126

Gnomad4 SAS exome AF: 0.227

Gnomad4 FIN exome AF: 0.117

Gnomad4 NFE exome AF: 0.117

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.206 AC: 31360 AN: 152048 Hom.: 4626 Cov.: 32 AF XY: 0.205 AC XY: 15229 AN XY: 74338

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.192

Alfa AF: 0.127 Hom.: 2421

Bravo AF: 0.218

Asia WGS AF: 0.190 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.51
DANN	Benign	0.46

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

Other links and lift over

dbSNP: rs33933482; hg19: chr1-206231264;