1-206110067-C-T

Variant names:

• chr1-206110067-C-T
• rs33933482
• NM_000707.5:c.*122G>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.*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
• Publications: 6 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=-0.84).
• 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	ENST00000367126.5	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

African (AFR) AF: 0.424 AC: 9939 AN: 23430

American (AMR) AF: 0.136 AC: 2629 AN: 19352

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 2308 AN: 17260

East Asian (EAS) AF: 0.126 AC: 4255 AN: 33874

South Asian (SAS) AF: 0.227 AC: 12850 AN: 56708

European-Finnish (FIN) AF: 0.117 AC: 5190 AN: 44264

Middle Eastern (MID) AF: 0.121 AC: 517 AN: 4282

European-Non Finnish (NFE) AF: 0.117 AC: 94792 AN: 811894

Other (OTH) AF: 0.143 AC: 6516 AN: 45588

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

African (AFR) AF: 0.416 AC: 17220 AN: 41404

American (AMR) AF: 0.149 AC: 2277 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3472

East Asian (EAS) AF: 0.104 AC: 537 AN: 5172

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4820

European-Finnish (FIN) AF: 0.110 AC: 1162 AN: 10600

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8160 AN: 67982

Other (OTH) AF: 0.192 AC: 406 AN: 2112

Alfa AF: 0.141 Hom.: 4651

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
PhyloP100		-0.68

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

Other links and lift over

dbSNP: rs33933482; hg19: chr1-206231264;