dbSNP rs3809114: INHBE:n.218-1238G>A (chr12-57454856-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000547970.1(INHBE):n.154G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 454,126 control chromosomes in the GnomAD database, including 55,972 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 0.44 ( 16324 hom., cov: 33)

Exomes 𝑓: 0.50 ( 39648 hom. )

Consequence

INHBE
ENST00000547970.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

Variant links:

Genes affected

INHBE (HGNC:24029): (inhibin subunit beta E) This gene encodes a member of the TGF-beta (transforming growth factor-beta) superfamily of proteins. The encoded preproprotein is proteolytically processed to generate an inhibin beta subunit. Inhibins have been implicated in regulating numerous cellular processes including cell proliferation, apoptosis, immune response and hormone secretion. This gene may be upregulated under conditions of endoplasmic reticulum stress, and this protein may inhibit cellular proliferation and growth in pancreas and liver. [provided by RefSeq, Sep 2016]

INHBE links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INHBE	ENST00000551553.1 link	n.218-1238G>A		intron_variant	Intron 1 of 2	1
INHBE	ENST00000547970.1 link	n.154G>A		non_coding_transcript_exon_variant	Exon 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.442

AC:

67208

AN:

152058

Hom.:

16321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.241

Gnomad AMI

AF:

0.702

Gnomad AMR

AF:

0.470

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.328

Gnomad SAS

AF:

0.423

Gnomad FIN

AF:

0.434

Gnomad MID

AF:

0.677

Gnomad NFE

AF:

0.557

Gnomad OTH

AF:

0.479

GnomAD4 exome

AF:

0.505

AC:

152349

AN:

301950

Hom.:

39648

Cov.:

AF XY:

0.502

AC XY:

86242

AN XY:

171956

show subpopulations

Gnomad4 AFR exome

AF:

0.235

Gnomad4 AMR exome

AF:

0.463

Gnomad4 ASJ exome

AF:

0.576

Gnomad4 EAS exome

AF:

0.320

Gnomad4 SAS exome

AF:

0.442

Gnomad4 FIN exome

AF:

0.461

Gnomad4 NFE exome

AF:

0.558

Gnomad4 OTH exome

AF:

0.503

GnomAD4 genome

AF:

0.442

AC:

67216

AN:

152176

Hom.:

16324

Cov.:

AF XY:

0.435

AC XY:

32385

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.241

Gnomad4 AMR

AF:

0.470

Gnomad4 ASJ

AF:

0.571

Gnomad4 EAS

AF:

0.329

Gnomad4 SAS

AF:

0.423

Gnomad4 FIN

AF:

0.434

Gnomad4 NFE

AF:

0.557

Gnomad4 OTH

AF:

0.474

Alfa

AF:

0.542

Hom.:

32979

Bravo

AF:

0.439

Asia WGS

AF:

0.338

AC:

1180

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.031

DANN

Benign

0.49

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over