chr7-41703060-T-C

Position:

• chr7-41703060-T-C

Variant summary

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

The NM_002192.4(INHBA):​c.-199A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 152,338 control chromosomes in the GnomAD database, including 328 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 0.055 (327 hom., cov: 32)
  • Exomes 𝑓: 0.22 (1 hom.)
• Consequence: INHBA NM_002192.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531

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]

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INHBA	NM_002192.4	c.-199A>G		5_prime_UTR_variant	1/3	ENST00000242208.5	NP_002183.1
INHBA-AS1	NR_027118.2	n.171-7538T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INHBA	ENST00000242208.5	c.-199A>G		5_prime_UTR_variant	1/3	1	NM_002192.4	ENSP00000242208	P1
INHBA-AS1	ENST00000415848.6	n.174-7538T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8424 AN: 152202 Hom.: 328 Cov.: 32

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0681

Gnomad ASJ AF: 0.0603

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.0549

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.0611

GnomAD4 exome AF: 0.222 AC: 4 AN: 18 Hom.: 1 Cov.: 0 AF XY: 0.286 AC XY: 4 AN XY: 14

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.0553 AC: 8424 AN: 152320 Hom.: 327 Cov.: 32 AF XY: 0.0539 AC XY: 4015 AN XY: 74500

Gnomad4 AFR AF: 0.0155

Gnomad4 AMR AF: 0.0682

Gnomad4 ASJ AF: 0.0603

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0251

Gnomad4 FIN AF: 0.0549

Gnomad4 NFE AF: 0.0825

Gnomad4 OTH AF: 0.0605

Alfa AF: 0.0687 Hom.: 89

Bravo AF: 0.0555

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs73100934; hg19: chr7-41742658;