3-39383736-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_017875.4(SLC25A38):c.12C>T(p.Asn4Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000689 in 1,614,194 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_017875.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A38 | NM_017875.4 | c.12C>T | p.Asn4Asn | synonymous_variant | Exon 1 of 7 | ENST00000650617.1 | NP_060345.2 | |
SLC25A38 | NM_001354798.2 | c.12C>T | p.Asn4Asn | synonymous_variant | Exon 1 of 6 | NP_001341727.1 | ||
LOC105377644 | XR_007096252.1 | n.85+505G>A | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000657 AC: 100AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000801 AC: 201AN: 250936Hom.: 1 AF XY: 0.000877 AC XY: 119AN XY: 135752
GnomAD4 exome AF: 0.000692 AC: 1012AN: 1461818Hom.: 3 Cov.: 30 AF XY: 0.000732 AC XY: 532AN XY: 727214
GnomAD4 genome AF: 0.000656 AC: 100AN: 152376Hom.: 0 Cov.: 33 AF XY: 0.000698 AC XY: 52AN XY: 74524
ClinVar
Submissions by phenotype
not provided Benign:3
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SLC25A38: BP4, BP7 -
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X-linked sideroblastic anemia 1 Uncertain:1
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Sideroblastic anemia 2 Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at