rs2108167

Variant names:

• chr7-41678509-T-G
• rs2108167
• ENST00000416150.1:n.53-10435A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416150.1(INHBA):​n.53-10435A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,116 control chromosomes in the GnomAD database, including 41,378 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 0.73 (41378 hom., cov: 33)
• Consequence: INHBA ENST00000416150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

Genes affected

INHBA (HGNC:6066): (inhibin subunit beta A) 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. The encoded protein also plays a role in eye, tooth and testis development. Elevated expression of this gene may be associated with cancer cachexia in human patients. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.749 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
INHBA	ENST00000416150.1	n.53-10435A>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111589 AN: 151998 Hom.: 41345 Cov.: 33

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.709

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.734 AC: 111667 AN: 152116 Hom.: 41378 Cov.: 33 AF XY: 0.733 AC XY: 54544 AN XY: 74364

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.704

Alfa AF: 0.755 Hom.: 7267

Bravo AF: 0.712

Asia WGS AF: 0.654 AC: 2272 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2108167; hg19: chr7-41718107;