rs73100934
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
NM_002192.4 5_prime_UTR
Scores
2
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]
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ACMG classification
Classification made for transcript
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 | UniProt |
---|---|---|---|---|---|---|---|
INHBA | NM_002192.4 | c.-199A>G | 5_prime_UTR_variant | 1/3 | ENST00000242208.5 | ||
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 | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INHBA | ENST00000242208.5 | c.-199A>G | 5_prime_UTR_variant | 1/3 | 1 | NM_002192.4 | P1 | ||
INHBA-AS1 | ENST00000415848.6 | n.174-7538T>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0553 AC: 8424AN: 152202Hom.: 328 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.222 AC: 4AN: 18Hom.: 1 Cov.: 0 AF XY: 0.286 AC XY: 4AN XY: 14
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GnomAD4 genome ? AF: 0.0553 AC: 8424AN: 152320Hom.: 327 Cov.: 32 AF XY: 0.0539 AC XY: 4015AN XY: 74500
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at