3-39383422-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_017875.4(SLC25A38):c.-303A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00559 in 423,062 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_017875.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A38 | NM_017875.4 | c.-303A>C | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000650617.1 | NP_060345.2 | ||
SLC25A38 | NM_001354798.2 | c.-303A>C | 5_prime_UTR_variant | Exon 1 of 6 | NP_001341727.1 | |||
LOC105377644 | XR_007096252.1 | n.86-378T>G | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0126 AC: 1923AN: 152124Hom.: 42 Cov.: 33
GnomAD4 exome AF: 0.00161 AC: 436AN: 270820Hom.: 9 Cov.: 0 AF XY: 0.00143 AC XY: 205AN XY: 143710
GnomAD4 genome AF: 0.0127 AC: 1930AN: 152242Hom.: 42 Cov.: 33 AF XY: 0.0122 AC XY: 909AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:2
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X-linked sideroblastic anemia 1 Benign:1
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Sideroblastic anemia 2 Benign: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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at