chr2-65021067-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1PM2BP4
The NM_003038.5(SLC1A4):c.1520C>T(p.Ser507Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000743 in 1,614,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S507S) has been classified as Likely benign.
Frequency
Consequence
NM_003038.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC1A4 | NM_003038.5 | c.1520C>T | p.Ser507Leu | missense_variant | 8/8 | ENST00000234256.4 | |
SLC1A4 | NM_001348406.2 | c.860C>T | p.Ser287Leu | missense_variant | 8/8 | ||
SLC1A4 | NM_001348407.2 | c.860C>T | p.Ser287Leu | missense_variant | 8/8 | ||
SLC1A4 | NM_001193493.2 | c.626C>T | p.Ser209Leu | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC1A4 | ENST00000234256.4 | c.1520C>T | p.Ser507Leu | missense_variant | 8/8 | 1 | NM_003038.5 | P1 | |
LINC02245 | ENST00000653778.1 | n.513+26887G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251108Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135716
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727242
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at