Genetic Variant ENST00000425896.1:n.44-122A>G (chr1-206117948-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000425896.1(AVPR1B-DT):n.44-122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,182 control chromosomes in the GnomAD database, including 5,397 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 0.18 ( 5396 hom., cov: 31)

Exomes 𝑓: 0.071 ( 1 hom. )

Consequence

AVPR1B-DT
ENST00000425896.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.249

Publications

7 publications found

Variant links:

Genes affected

AVPR1B-DT (HGNC:55832): (AVPR1B divergent transcript)

AVPR1B-DT links:

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 = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AVPR1B-DT	NR_186693.1 link	n.44-122A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AVPR1B-DT	ENST00000425896.1 link	n.44-122A>G		intron_variant	Intron 1 of 2	3
AVPR1B	ENST00000612906.1 link	n.-249T>C		upstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27001

AN:

151924

Hom.:

5375

Cov.:

show subpopulations

Gnomad AFR

AF:

0.500

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.0839

Gnomad ASJ

AF:

0.0982

Gnomad EAS

AF:

0.0162

Gnomad SAS

AF:

0.0555

Gnomad FIN

AF:

0.0681

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.0481

Gnomad OTH

AF:

0.149

GnomAD4 exome

AF:

0.0714

AC:

AN:

140

Hom.:

Cov.:

AF XY:

0.0581

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.125

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0395

AC:

AN:

Other (OTH)

AF:

0.0500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.178

AC:

27064

AN:

152042

Hom.:

5396

Cov.:

AF XY:

0.173

AC XY:

12855

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.500

AC:

20715

AN:

41424

American (AMR)

AF:

0.0838

AC:

1281

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0982

AC:

340

AN:

3464

East Asian (EAS)

AF:

0.0162

AC:

AN:

5172

South Asian (SAS)

AF:

0.0551

AC:

266

AN:

4826

European-Finnish (FIN)

AF:

0.0681

AC:

722

AN:

10596

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0481

AC:

3272

AN:

67966

Other (OTH)

AF:

0.147

AC:

309

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

812

1623

2435

3246

4058

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

240

480

720

960

1200

<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:

0.116

Hom.:

5021

Bravo

AF:

0.195

Asia WGS

AF:

0.0610

AC:

214

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

7.3

(source)

DANN

Benign

0.47

PhyloP100

0.25

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