chr15-48121072-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_205850.3(SLC24A5):c.28G>C(p.Ala10Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A10V) has been classified as Uncertain significance.
Frequency
Consequence
NM_205850.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC24A5 | NM_205850.3 | c.28G>C | p.Ala10Pro | missense_variant | 1/9 | ENST00000341459.8 | |
SLC24A5 | XM_047432394.1 | c.28G>C | p.Ala10Pro | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC24A5 | ENST00000341459.8 | c.28G>C | p.Ala10Pro | missense_variant | 1/9 | 1 | NM_205850.3 | P1 | |
SLC24A5 | ENST00000449382.2 | c.28G>C | p.Ala10Pro | missense_variant | 1/8 | 1 | |||
SLC24A5 | ENST00000482911.2 | c.28G>C | p.Ala10Pro | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000788 AC: 120AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000148 AC: 37AN: 250598Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135428
GnomAD4 exome AF: 0.0000609 AC: 89AN: 1461632Hom.: 0 Cov.: 30 AF XY: 0.0000426 AC XY: 31AN XY: 727114
GnomAD4 genome ? AF: 0.000788 AC: 120AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000900 AC XY: 67AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at