chr5-139379831-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005847.5(SLC23A1):c.772A>G(p.Met258Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00365 in 1,613,970 control chromosomes in the GnomAD database, including 202 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005847.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC23A1 | NM_005847.5 | c.772A>G | p.Met258Val | missense_variant | 8/15 | ENST00000348729.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC23A1 | ENST00000348729.8 | c.772A>G | p.Met258Val | missense_variant | 8/15 | 1 | NM_005847.5 | P1 | |
SLC23A1 | ENST00000353963.7 | c.784A>G | p.Met262Val | missense_variant | 8/15 | 1 | |||
SLC23A1 | ENST00000504513.1 | c.164+125A>G | intron_variant | 5 | |||||
SLC23A1 | ENST00000506512.1 | n.383A>G | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0194 AC: 2943AN: 151978Hom.: 102 Cov.: 32
GnomAD3 exomes AF: 0.00506 AC: 1271AN: 251322Hom.: 39 AF XY: 0.00374 AC XY: 508AN XY: 135840
GnomAD4 exome AF: 0.00200 AC: 2922AN: 1461874Hom.: 94 Cov.: 33 AF XY: 0.00171 AC XY: 1247AN XY: 727240
GnomAD4 genome ? AF: 0.0195 AC: 2971AN: 152096Hom.: 108 Cov.: 32 AF XY: 0.0184 AC XY: 1369AN XY: 74334
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at