7-41703696-T-C

Variant names:

• chr7-41703696-T-C
• rs2877098
• ENST00000415848.6:n.174-6902T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000947876.1(INHBA):​c.-144+1588A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,720 control chromosomes in the GnomAD database, including 36,660 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 0.69 (36660 hom., cov: 30)
• Consequence: INHBA ENST00000947876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 13 publications found

Genes affected

INHBA-AS1 (HGNC:40303): (INHBA antisense RNA 1)

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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000947876.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBA-AS1	NR_027118.2		n.171-6902T>C		intron	N/A
	INHBA-AS1	NR_027119.2		n.171-6902T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBA-AS1	ENST00000415848.6	TSL:1	n.174-6902T>C		intron	N/A
	INHBA-AS1	ENST00000420821.2	TSL:1	n.161-6902T>C		intron	N/A
	INHBA	ENST00000638023.1	TSL:5	c.-225-610A>G		intron	N/A	ENSP00000490646.1

Frequencies

GnomAD3 genomes AF: 0.693 AC: 104987 AN: 151602 Hom.: 36625 Cov.: 30

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.693 AC: 105068 AN: 151720 Hom.: 36660 Cov.: 30 AF XY: 0.694 AC XY: 51469 AN XY: 74122

African (AFR) AF: 0.740 AC: 30570 AN: 41316

American (AMR) AF: 0.578 AC: 8806 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2190 AN: 3470

East Asian (EAS) AF: 0.606 AC: 3123 AN: 5152

South Asian (SAS) AF: 0.695 AC: 3343 AN: 4810

European-Finnish (FIN) AF: 0.779 AC: 8174 AN: 10490

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.685 AC: 46575 AN: 67946

Other (OTH) AF: 0.657 AC: 1380 AN: 2100

Alfa AF: 0.680 Hom.: 78472

Bravo AF: 0.674

Asia WGS AF: 0.661 AC: 2294 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.2
DANN	Benign	0.72
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2877098; hg19: chr7-41743294;