Genetic Variant ENSG00000287200:n.268C>G (chr12-57459370-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000656936.1(ENSG00000287200):n.268C>G 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 0.591 in 152,218 control chromosomes in the GnomAD database, including 27,031 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 0.59 ( 26960 hom., cov: 30)

Exomes 𝑓: 0.63 ( 71 hom. )

Consequence

ENSG00000287200
ENST00000656936.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Publications

12 publications found

Variant links:

Genes affected

ENSG00000287200 (HGNC:):

ENSG00000287200 links:

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 was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902947	XR_007063335.1 link	n.422C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287200	ENST00000656936.1 link	n.268C>G	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000287200	ENST00000781819.1 link	n.276C>G	non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000287200	ENST00000781821.1 link	n.280C>G	non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.591

AC:

89740

AN:

151736

Hom.:

26951

Cov.:

show subpopulations

Gnomad AFR

AF:

0.510

Gnomad AMI

AF:

0.651

Gnomad AMR

AF:

0.580

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.523

Gnomad SAS

AF:

0.494

Gnomad FIN

AF:

0.525

Gnomad MID

AF:

0.801

Gnomad NFE

AF:

0.659

Gnomad OTH

AF:

0.631

GnomAD4 exome

AF:

0.626

AC:

228

AN:

364

Hom.:

AF XY:

0.650

AC XY:

156

AN XY:

240

show subpopulations

African (AFR)

AF:

0.583

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.530

AC:

AN:

134

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.691

AC:

134

AN:

194

Other (OTH)

AF:

0.714

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

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:

0.591

AC:

89764

AN:

151854

Hom.:

26960

Cov.:

AF XY:

0.584

AC XY:

43301

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.510

AC:

21114

AN:

41408

American (AMR)

AF:

0.580

AC:

8854

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.669

AC:

2316

AN:

3462

East Asian (EAS)

AF:

0.524

AC:

2687

AN:

5132

South Asian (SAS)

AF:

0.494

AC:

2375

AN:

4804

European-Finnish (FIN)

AF:

0.525

AC:

5533

AN:

10530

Middle Eastern (MID)

AF:

0.796

AC:

234

AN:

294

European-Non Finnish (NFE)

AF:

0.659

AC:

44741

AN:

67930

Other (OTH)

AF:

0.625

AC:

1319

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1840

3679

5519

7358

9198

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

754

1508

2262

3016

3770

<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:

0.474

Hom.:

1257

Bravo

AF:

0.593

Asia WGS

AF:

0.469

AC:

1634

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

6.9

(source)

DANN

Benign

0.69

PhyloP100

0.24

PromoterAI

0.013

Neutral

(source)

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