Genetic Variant NM_000707.5: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:

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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

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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