chr14-36684767-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030631.4(SLC25A21):c.762G>T(p.Met254Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 1,605,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M254L) has been classified as Uncertain significance.
Frequency
Consequence
NM_030631.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A21 | NM_030631.4 | c.762G>T | p.Met254Ile | missense_variant | 8/10 | ENST00000331299.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A21 | ENST00000331299.6 | c.762G>T | p.Met254Ile | missense_variant | 8/10 | 1 | NM_030631.4 | P4 | |
SLC25A21 | ENST00000555449.5 | c.762G>T | p.Met254Ile | missense_variant | 8/11 | 2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244708Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132106
GnomAD4 exome AF: 0.0000131 AC: 19AN: 1453920Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 722866
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74244
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 28, 2023 | The c.762G>T (p.M254I) alteration is located in exon 8 (coding exon 8) of the SLC25A21 gene. This alteration results from a G to T substitution at nucleotide position 762, causing the methionine (M) at amino acid position 254 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at