chr7-41678509-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.752 AC: 31223 AN: 41500

American (AMR) AF: 0.605 AC: 9245 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2313 AN: 3466

East Asian (EAS) AF: 0.607 AC: 3138 AN: 5166

South Asian (SAS) AF: 0.671 AC: 3228 AN: 4814

European-Finnish (FIN) AF: 0.836 AC: 8839 AN: 10578

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51272 AN: 67990

Other (OTH) AF: 0.704 AC: 1486 AN: 2112

Alfa AF: 0.740 Hom.: 13902

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
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2108167; hg19: chr7-41718107;