chr14-36680661-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_030631.4(SLC25A21):c.897G>T(p.Trp299Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00531 in 1,612,392 control chromosomes in the GnomAD database, including 354 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_030631.4 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A21 | NM_030631.4 | c.897G>T | p.Trp299Cys | missense_variant | 10/10 | ENST00000331299.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A21 | ENST00000331299.6 | c.897G>T | p.Trp299Cys | missense_variant | 10/10 | 1 | NM_030631.4 | P4 | |
SLC25A21 | ENST00000555449.5 | c.896+1G>T | splice_donor_variant | 2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0267 AC: 4056AN: 152086Hom.: 173 Cov.: 32
GnomAD3 exomes AF: 0.00713 AC: 1778AN: 249510Hom.: 69 AF XY: 0.00546 AC XY: 736AN XY: 134898
GnomAD4 exome AF: 0.00308 AC: 4493AN: 1460188Hom.: 182 Cov.: 31 AF XY: 0.00280 AC XY: 2031AN XY: 726300
GnomAD4 genome AF: 0.0267 AC: 4065AN: 152204Hom.: 172 Cov.: 32 AF XY: 0.0260 AC XY: 1932AN XY: 74398
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at