chr5-102249735-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_180991.5(SLCO4C1):c.1523C>T(p.Ser508Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,613,836 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 (★).
Frequency
Consequence
NM_180991.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO4C1 | NM_180991.5 | c.1523C>T | p.Ser508Leu | missense_variant | 9/13 | ENST00000310954.7 | |
SLCO4C1 | XM_011543370.3 | c.1259C>T | p.Ser420Leu | missense_variant | 8/12 | ||
SLCO4C1 | XM_011543372.2 | c.1109C>T | p.Ser370Leu | missense_variant | 11/15 | ||
SLCO4C1 | XM_047417146.1 | c.1109C>T | p.Ser370Leu | missense_variant | 11/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO4C1 | ENST00000310954.7 | c.1523C>T | p.Ser508Leu | missense_variant | 9/13 | 1 | NM_180991.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000638 AC: 16AN: 250860Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135568
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461634Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727118
GnomAD4 genome AF: 0.000210 AC: 32AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74390
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at