rs10512174
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030940.4(ISCA1):c.241+348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,980 control chromosomes in the GnomAD database, including 15,248 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 0.45 ( 15248 hom., cov: 32)
Consequence
ISCA1
NM_030940.4 intron
NM_030940.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.739
Genes affected
ISCA1 (HGNC:28660): (iron-sulfur cluster assembly 1) ISCA1 is a mitochondrial protein involved in the biogenesis and assembly of iron-sulfur clusters, which play a role in electron-transfer reactions (Cozar-Castellano et al., 2004 [PubMed 15262227]).[supplied by OMIM, Mar 2008]
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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=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISCA1 | NM_030940.4 | c.241+348G>A | intron_variant | ENST00000375991.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISCA1 | ENST00000375991.9 | c.241+348G>A | intron_variant | 1 | NM_030940.4 | P1 | |||
ISCA1 | ENST00000311534.6 | c.-54+348G>A | intron_variant | 2 | |||||
ISCA1 | ENST00000326094.4 | c.241+348G>A | intron_variant | 3 | |||||
ISCA1 | ENST00000637705.1 | c.178+348G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.445 AC: 67604AN: 151864Hom.: 15225 Cov.: 32
GnomAD3 genomes
?
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.445 AC: 67673AN: 151980Hom.: 15248 Cov.: 32 AF XY: 0.440 AC XY: 32656AN XY: 74262
GnomAD4 genome
?
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67673
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151980
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32
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32656
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74262
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1717
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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