dbSNP rs57802235: INHBB:c.*1994G>A (chr2-120351868-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002193.4(INHBB):c.*1994G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,220 control chromosomes in the GnomAD database, including 1,811 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 0.12 ( 1811 hom., cov: 33)

Exomes 𝑓: 0.071 ( 0 hom. )

Consequence

INHBB
NM_002193.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.39

Variant links:

Genes affected

INHBB (HGNC:6067): (inhibin subunit beta B) This gene encodes a member of the TGF-beta (transforming growth factor-beta) superfamily of proteins. The encoded preproprotein is proteolytically processed to generate a subunit of the dimeric activin and inhibin protein complexes. These complexes activate and inhibit, respectively, follicle stimulating hormone secretion from the pituitary gland. Polymorphisms near this gene are associated with pre-eclampsia in female human patients. [provided by RefSeq, Aug 2016]

INHBB 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INHBB	NM_002193.4 link	c.*1994G>A		downstream_gene_variant		ENST00000295228.4	NP_002184.2	P09529

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INHBB	ENST00000295228.4 link	c.*1994G>A		downstream_gene_variant		1	NM_002193.4	ENSP00000295228.3		P09529

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18174

AN:

152074

Hom.:

1806

Cov.:

show subpopulations

Gnomad AFR

AF:

0.203

Gnomad AMI

AF:

0.100

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.0245

Gnomad EAS

AF:

0.446

Gnomad SAS

AF:

0.0634

Gnomad FIN

AF:

0.0788

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0486

Gnomad OTH

AF:

0.0852

GnomAD4 exome

AF:

0.0714

AC:

AN:

Hom.:

AF XY:

0.0625

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.120

AC:

18202

AN:

152192

Hom.:

1811

Cov.:

AF XY:

0.123

AC XY:

9177

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.203

Gnomad4 AMR

AF:

0.173

Gnomad4 ASJ

AF:

0.0245

Gnomad4 EAS

AF:

0.446

Gnomad4 SAS

AF:

0.0632

Gnomad4 FIN

AF:

0.0788

Gnomad4 NFE

AF:

0.0486

Gnomad4 OTH

AF:

0.0881

Alfa

AF:

0.0771

Hom.:

134

Bravo

AF:

0.136

Asia WGS

AF:

0.221

AC:

768

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

DANN

Benign

0.74

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