chr21-42539529-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001320537.2(SLC37A1):c.368G>A(p.Arg123His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,612,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R123C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001320537.2 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 |
---|---|---|---|---|---|---|---|
SLC37A1 | NM_001320537.2 | c.368G>A | p.Arg123His | missense_variant | 6/20 | ENST00000352133.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC37A1 | ENST00000352133.3 | c.368G>A | p.Arg123His | missense_variant | 6/20 | 1 | NM_001320537.2 | P1 | |
SLC37A1 | ENST00000398341.7 | c.368G>A | p.Arg123His | missense_variant | 7/21 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000801 AC: 20AN: 249554Hom.: 0 AF XY: 0.0000741 AC XY: 10AN XY: 134880
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1460314Hom.: 0 Cov.: 30 AF XY: 0.0000551 AC XY: 40AN XY: 726444
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.368G>A (p.R123H) alteration is located in exon 7 (coding exon 5) of the SLC37A1 gene. This alteration results from a G to A substitution at nucleotide position 368, causing the arginine (R) at amino acid position 123 to be replaced by a histidine (H). 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