1-206110180-G-C

Variant names:

• chr1-206110180-G-C
• rs33976516
• NM_000707.5:c.*9C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000707.5(AVPR1B):​c.*9C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 1,598,026 control chromosomes in the GnomAD database, including 1,765 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 0.063 (431 hom., cov: 32)
  • Exomes 𝑓: 0.036 (1334 hom.)
• Consequence: AVPR1B NM_000707.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AVPR1B	NM_000707.5	MANE Select	c.*9C>G		3_prime_UTR	Exon 2 of 2	NP_000698.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AVPR1B	ENST00000367126.5	TSL:1 MANE Select	c.*9C>G		3_prime_UTR	Exon 2 of 2	ENSP00000356094.4
	AVPR1B	ENST00000612906.1	TSL:4	n.380C>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9525 AN: 152160 Hom.: 428 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0281

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0365

Gnomad OTH AF: 0.0603

GnomAD2 exomes AF: 0.0418 AC: 10051 AN: 240452 AF XY: 0.0413

Gnomad AFR exome AF: 0.128

Gnomad AMR exome AF: 0.0276

Gnomad ASJ exome AF: 0.0960

Gnomad EAS exome AF: 0.00140

Gnomad FIN exome AF: 0.0441

Gnomad NFE exome AF: 0.0388

Gnomad OTH exome AF: 0.0484

GnomAD4 exome AF: 0.0360 AC: 52004 AN: 1445748 Hom.: 1334 Cov.: 32 AF XY: 0.0359 AC XY: 25729 AN XY: 716536

African (AFR) AF: 0.131 AC: 4330 AN: 33088

American (AMR) AF: 0.0293 AC: 1280 AN: 43620

Ashkenazi Jewish (ASJ) AF: 0.0920 AC: 2331 AN: 25346

East Asian (EAS) AF: 0.00216 AC: 85 AN: 39368

South Asian (SAS) AF: 0.0291 AC: 2465 AN: 84772

European-Finnish (FIN) AF: 0.0437 AC: 2318 AN: 53022

Middle Eastern (MID) AF: 0.104 AC: 590 AN: 5690

European-Non Finnish (NFE) AF: 0.0327 AC: 35965 AN: 1101266

Other (OTH) AF: 0.0443 AC: 2640 AN: 59576

GnomAD4 genome AF: 0.0627 AC: 9545 AN: 152278 Hom.: 431 Cov.: 32 AF XY: 0.0612 AC XY: 4560 AN XY: 74462

African (AFR) AF: 0.127 AC: 5293 AN: 41540

American (AMR) AF: 0.0397 AC: 607 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0873 AC: 303 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.0279 AC: 135 AN: 4832

European-Finnish (FIN) AF: 0.0507 AC: 538 AN: 10604

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0365 AC: 2486 AN: 68026

Other (OTH) AF: 0.0597 AC: 126 AN: 2112

Alfa AF: 0.0338 Hom.: 36

Bravo AF: 0.0655

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.5
DANN	Benign	0.66
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs33976516; hg19: chr1-206231151;