17-4937874-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_003562.5(SLC25A11):c.812G>A(p.Arg271His) variant causes a missense change. The variant allele was found at a frequency of 0.00000558 in 1,613,614 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R271C) has been classified as Uncertain significance.
Frequency
Consequence
NM_003562.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A11 | NM_003562.5 | c.812G>A | p.Arg271His | missense_variant | Exon 8 of 8 | ENST00000225665.12 | NP_003553.2 | |
SLC25A11 | NM_001165417.2 | c.779G>A | p.Arg260His | missense_variant | Exon 8 of 8 | NP_001158889.1 | ||
SLC25A11 | NM_001165418.2 | c.659G>A | p.Arg220His | missense_variant | Exon 7 of 7 | NP_001158890.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A11 | ENST00000225665.12 | c.812G>A | p.Arg271His | missense_variant | Exon 8 of 8 | 1 | NM_003562.5 | ENSP00000225665.7 | ||
SLC25A11 | ENST00000576951.1 | c.779G>A | p.Arg260His | missense_variant | Exon 8 of 8 | 5 | ENSP00000458993.1 | |||
SLC25A11 | ENST00000544061.6 | c.659G>A | p.Arg220His | missense_variant | Exon 7 of 7 | 3 | ENSP00000440804.2 | |||
SLC25A11 | ENST00000574710.1 | n.1619G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250080Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135176
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461308Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726932
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.812G>A (p.R271H) alteration is located in exon 8 (coding exon 8) of the SLC25A11 gene. This alteration results from a G to A substitution at nucleotide position 812, causing the arginine (R) at amino acid position 271 to be replaced by a histidine (H). 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