chr5-110748269-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000355943.8(SLC25A46):c.563+6A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,608,406 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000355943.8 splice_region, intron
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A46 | NM_138773.4 | c.563+6A>T | splice_region_variant, intron_variant | ENST00000355943.8 | NP_620128.1 | |||
SLC25A46 | NM_001303249.3 | c.563+6A>T | splice_region_variant, intron_variant | NP_001290178.1 | ||||
SLC25A46 | NM_001303250.3 | c.290+6A>T | splice_region_variant, intron_variant | NP_001290179.1 | ||||
SLC25A46 | NR_138151.2 | n.676+6A>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A46 | ENST00000355943.8 | c.563+6A>T | splice_region_variant, intron_variant | 1 | NM_138773.4 | ENSP00000348211.3 |
Frequencies
GnomAD3 genomes AF: 0.0121 AC: 1833AN: 152086Hom.: 45 Cov.: 32
GnomAD3 exomes AF: 0.00315 AC: 790AN: 251152Hom.: 16 AF XY: 0.00235 AC XY: 319AN XY: 135766
GnomAD4 exome AF: 0.00118 AC: 1721AN: 1456202Hom.: 28 Cov.: 27 AF XY: 0.00102 AC XY: 742AN XY: 724870
GnomAD4 genome AF: 0.0121 AC: 1840AN: 152204Hom.: 46 Cov.: 32 AF XY: 0.0124 AC XY: 924AN XY: 74412
ClinVar
Submissions by phenotype
Neuropathy, hereditary motor and sensory, type 6B Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at