chr6-46671128-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_004277.5(SLC25A27):c.800G>A(p.Gly267Glu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000114 in 1,584,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004277.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A27 | NM_004277.5 | c.800G>A | p.Gly267Glu | missense_variant, splice_region_variant | 8/9 | ENST00000371347.10 | |
TDRD6-AS1 | NR_134643.1 | n.233-543C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A27 | ENST00000371347.10 | c.800G>A | p.Gly267Glu | missense_variant, splice_region_variant | 8/9 | 1 | NM_004277.5 | P1 | |
TDRD6-AS1 | ENST00000434329.2 | n.233-543C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000870 AC: 2AN: 229858Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 124916
GnomAD4 exome AF: 0.0000119 AC: 17AN: 1432580Hom.: 0 Cov.: 27 AF XY: 0.0000140 AC XY: 10AN XY: 712908
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2022 | The c.800G>A (p.G267E) alteration is located in exon 8 (coding exon 8) of the SLC25A27 gene. This alteration results from a G to A substitution at nucleotide position 800, causing the glycine (G) at amino acid position 267 to be replaced by a glutamic acid (E). 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