Genetic Variant AVPR1B:c.*117A>G (chr1-206110072-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000707.5(AVPR1B):c.*117A>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 0.178 in 1,246,046 control chromosomes in the GnomAD database, including 25,395 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 0.27 ( 7634 hom., cov: 32)

Exomes 𝑓: 0.17 ( 17761 hom. )

Consequence

AVPR1B
NM_000707.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0350

Publications

9 publications found

Variant links:

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]

AVPR1B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AVPR1B	NM_000707.5 link	c.*117A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000367126.5	NP_000698.1	P47901

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AVPR1B	ENST00000367126.5 link	c.*117A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_000707.5	ENSP00000356094.4		P47901
AVPR1B	ENST00000612906.1 link	n.488A>G		non_coding_transcript_exon_variant	Exon 2 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.267

AC:

40574

AN:

151900

Hom.:

7619

Cov.:

show subpopulations

Gnomad AFR

AF:

0.538

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.254

GnomAD4 exome

AF:

0.166

AC:

181333

AN:

1094028

Hom.:

17761

Cov.:

AF XY:

0.168

AC XY:

90415

AN XY:

537760

show subpopulations

African (AFR)

AF:

0.547

AC:

13215

AN:

24174

American (AMR)

AF:

0.170

AC:

3399

AN:

19964

Ashkenazi Jewish (ASJ)

AF:

0.222

AC:

3894

AN:

17566

East Asian (EAS)

AF:

0.127

AC:

4393

AN:

34622

South Asian (SAS)

AF:

0.255

AC:

14976

AN:

58738

European-Finnish (FIN)

AF:

0.161

AC:

7203

AN:

44856

Middle Eastern (MID)

AF:

0.218

AC:

969

AN:

4440

European-Non Finnish (NFE)

AF:

0.148

AC:

124595

AN:

842770

Other (OTH)

AF:

0.185

AC:

8689

AN:

46898

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

7225

14449

21674

28898

36123

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4394

8788

13182

17576

21970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.267

AC:

40636

AN:

152018

Hom.:

7634

Cov.:

AF XY:

0.265

AC XY:

19667

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.538

AC:

22284

AN:

41386

American (AMR)

AF:

0.187

AC:

2865

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.215

AC:

746

AN:

3472

East Asian (EAS)

AF:

0.106

AC:

548

AN:

5174

South Asian (SAS)

AF:

0.251

AC:

1211

AN:

4816

European-Finnish (FIN)

AF:

0.160

AC:

1699

AN:

10590

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.156

AC:

10634

AN:

67968

Other (OTH)

AF:

0.250

AC:

528

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1332

2664

3997

5329

6661

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

386

772

1158

1544

1930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.177

Hom.:

6006

Bravo

AF:

0.281

Asia WGS

AF:

0.208

AC:

727

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.6

(source)

DANN

Benign

0.31

PhyloP100

0.035

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over