21-42539610-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001320537.2(SLC37A1):c.449A>G(p.Tyr150Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001320537.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC37A1 | NM_001320537.2 | c.449A>G | p.Tyr150Cys | missense_variant | 6/20 | ENST00000352133.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC37A1 | ENST00000352133.3 | c.449A>G | p.Tyr150Cys | missense_variant | 6/20 | 1 | NM_001320537.2 | P1 | |
SLC37A1 | ENST00000398341.7 | c.449A>G | p.Tyr150Cys | missense_variant | 7/21 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250976Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135630
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461630Hom.: 0 Cov.: 30 AF XY: 0.0000316 AC XY: 23AN XY: 727120
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 04, 2022 | The c.449A>G (p.Y150C) alteration is located in exon 7 (coding exon 5) of the SLC37A1 gene. This alteration results from a A to G substitution at nucleotide position 449, causing the tyrosine (Y) at amino acid position 150 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at