chr7-41678509-T-G

Position:

• chr7-41678509-T-G

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INHBA	ENST00000416150.1	n.53-10435A>C		intron_variant, non_coding_transcript_variant		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;