rs2877098

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr7-41703696-T-A
• chr7-41703696-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000638023.1(INHBA):​c.-225-610A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: INHBA ENST00000638023.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INHBA	XM_017012174.2	c.-144+1588A>T		intron_variant	Intron 1 of 2		XP_016867663.2
INHBA	XM_047420335.1	c.-144+1033A>T		intron_variant	Intron 2 of 3		XP_047276291.1
INHBA-AS1	NR_027118.2	n.171-6902T>A		intron_variant	Intron 1 of 3
INHBA-AS1	NR_027119.2	n.171-6902T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INHBA-AS1	ENST00000415848.6	n.174-6902T>A		intron_variant	Intron 1 of 3	1
INHBA-AS1	ENST00000420821.2	n.161-6902T>A		intron_variant	Intron 1 of 2	1
INHBA	ENST00000638023.1	c.-225-610A>T		intron_variant	Intron 2 of 4	5		ENSP00000490646.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	6.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2877098; hg19: chr7-41743294;