7-41703696-T-C

Position:

• chr7-41703696-T-C

Variant summary

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

The NR_027118.2(INHBA-AS1):​n.171-6902T>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 0.693 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-AS1 NR_027118.2 intron, non_coding_transcript
• 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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INHBA-AS1	NR_027118.2	n.171-6902T>C		intron_variant, non_coding_transcript_variant
INHBA	XM_017012174.2	c.-144+1588A>G		intron_variant			XP_016867663.2
INHBA	XM_047420335.1	c.-144+1033A>G		intron_variant			XP_047276291.1
INHBA-AS1	NR_027119.2	n.171-6902T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INHBA-AS1	ENST00000415848.6	n.174-6902T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.657

Alfa AF: 0.677 Hom.: 48682

Bravo AF: 0.674

Asia WGS AF: 0.661 AC: 2294 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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;