rs1426654
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_205850.3(SLC24A5):c.331A>G(p.Thr111Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,613,472 control chromosomes in the GnomAD database, including 59,639 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_205850.3 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
SLC24A5 | NM_205850.3 | c.331A>G | p.Thr111Ala | missense_variant | 3/9 | ENST00000341459.8 | |
SLC24A5 | XM_047432394.1 | c.331A>G | p.Thr111Ala | missense_variant | 3/8 | ||
SLC24A5 | XM_024449901.2 | c.-9A>G | 5_prime_UTR_variant | 2/8 | |||
SLC24A5 | XM_047432395.1 | c.-9A>G | 5_prime_UTR_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC24A5 | ENST00000341459.8 | c.331A>G | p.Thr111Ala | missense_variant | 3/9 | 1 | NM_205850.3 | P1 | |
SLC24A5 | ENST00000449382.2 | c.151A>G | p.Thr51Ala | missense_variant | 2/8 | 1 | |||
SLC24A5 | ENST00000463289.1 | n.91A>G | non_coding_transcript_exon_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.298 AC: 45263AN: 152008Hom.: 17249 Cov.: 32
GnomAD3 exomes AF: 0.230 AC: 57776AN: 251246Hom.: 21227 AF XY: 0.196 AC XY: 26657AN XY: 135786
GnomAD4 exome AF: 0.0806 AC: 117787AN: 1461346Hom.: 42311 Cov.: 31 AF XY: 0.0786 AC XY: 57143AN XY: 726986
GnomAD4 genome ? AF: 0.299 AC: 45411AN: 152126Hom.: 17328 Cov.: 32 AF XY: 0.301 AC XY: 22390AN XY: 74392
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 25, 2020 | This variant is associated with the following publications: (PMID: 17999355, 18650849, 24244186, 23071798, 16357253, 29025994, 31315583) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at