rs1569767
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020689.4(SLC24A3):c.163G>A(p.Val55Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 1,613,002 control chromosomes in the GnomAD database, including 150,187 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_020689.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC24A3 | NM_020689.4 | c.163G>A | p.Val55Ile | missense_variant | 2/17 | ENST00000328041.11 | |
SLC24A3-AS1 | NR_024564.1 | n.529+2160C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC24A3 | ENST00000328041.11 | c.163G>A | p.Val55Ile | missense_variant | 2/17 | 1 | NM_020689.4 | P1 | |
SLC24A3-AS1 | ENST00000319682.2 | n.529+2160C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.408 AC: 61977AN: 151774Hom.: 13103 Cov.: 31
GnomAD3 exomes AF: 0.440 AC: 110152AN: 250206Hom.: 24944 AF XY: 0.440 AC XY: 59562AN XY: 135232
GnomAD4 exome AF: 0.430 AC: 628491AN: 1461110Hom.: 137079 Cov.: 50 AF XY: 0.430 AC XY: 312843AN XY: 726796
GnomAD4 genome ? AF: 0.408 AC: 62024AN: 151892Hom.: 13108 Cov.: 31 AF XY: 0.409 AC XY: 30382AN XY: 74234
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at