1-206110180-G-C

Variant names:

• chr1-206110180-G-C
• rs33976516
• ENST00000367126:c.*9C>G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AVPR1B	NM_000707.5	c.*9C>G		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.*9C>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_000707.5	ENSP00000356094.4
AVPR1B	ENST00000612906.1	n.380C>G		non_coding_transcript_exon_variant	Exon 2 of 2	4

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

GnomAD3 exomes AF: 0.0418 AC: 10051 AN: 240452 Hom.: 315 AF XY: 0.0413 AC XY: 5393 AN XY: 130520

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 SAS exome AF: 0.0289

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

Gnomad4 AFR exome AF: 0.131

Gnomad4 AMR exome AF: 0.0293

Gnomad4 ASJ exome AF: 0.0920

Gnomad4 EAS exome AF: 0.00216

Gnomad4 SAS exome AF: 0.0291

Gnomad4 FIN exome AF: 0.0437

Gnomad4 NFE exome AF: 0.0327

Gnomad4 OTH exome AF: 0.0443

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

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0397

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0279

Gnomad4 FIN AF: 0.0507

Gnomad4 NFE AF: 0.0365

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0338 Hom.: 36

Bravo AF: 0.0655

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs33976516; hg19: chr1-206231151;