rs3741414
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005538.4(INHBC):c.*244C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 376,874 control chromosomes in the GnomAD database, including 8,261 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 0.19 ( 3106 hom., cov: 32)
Exomes 𝑓: 0.20 ( 5155 hom. )
Consequence
INHBC
NM_005538.4 3_prime_UTR
NM_005538.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.530
Genes affected
INHBC (HGNC:6068): (inhibin subunit beta C) 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 homodimeric and heterodimeric activin complexes. The heterodimeric complex may function in the inhibition of activin A signaling. Transgenic mice overexpressing this gene exhibit defects in testis, liver and prostate. [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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INHBC | NM_005538.4 | c.*244C>T | 3_prime_UTR_variant | 2/2 | ENST00000309668.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INHBC | ENST00000309668.3 | c.*244C>T | 3_prime_UTR_variant | 2/2 | 1 | NM_005538.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.186 AC: 28226AN: 151924Hom.: 3095 Cov.: 32
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GnomAD4 exome AF: 0.203 AC: 45708AN: 224832Hom.: 5155 Cov.: 4 AF XY: 0.200 AC XY: 22707AN XY: 113644
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GnomAD4 genome ? AF: 0.186 AC: 28250AN: 152042Hom.: 3106 Cov.: 32 AF XY: 0.183 AC XY: 13584AN XY: 74326
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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