21-42518479-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001320537.2(SLC37A1):c.25C>T(p.Arg9Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000215 in 1,614,116 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts 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
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000422 AC: 106AN: 251466Hom.: 0 AF XY: 0.000544 AC XY: 74AN XY: 135916
GnomAD4 exome AF: 0.000211 AC: 308AN: 1461860Hom.: 6 Cov.: 31 AF XY: 0.000283 AC XY: 206AN XY: 727232
GnomAD4 genome AF: 0.000256 AC: 39AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.25C>T (p.R9C) alteration is located in exon 3 (coding exon 1) of the SLC37A1 gene. This alteration results from a C to T substitution at nucleotide position 25, causing the arginine (R) at amino acid position 9 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