chr21-42539564-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001320537.2(SLC37A1):c.403C>T(p.Leu135Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000744 in 1,613,844 control chromosomes in the GnomAD database, including 9 homozygotes. 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 (★). Synonymous variant affecting the same amino acid position (i.e. L135L) has been classified as Benign.
Frequency
Consequence
NM_001320537.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC37A1 | NM_001320537.2 | c.403C>T | p.Leu135Phe | missense_variant | 6/20 | ENST00000352133.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC37A1 | ENST00000352133.3 | c.403C>T | p.Leu135Phe | missense_variant | 6/20 | 1 | NM_001320537.2 | P1 | |
SLC37A1 | ENST00000398341.7 | c.403C>T | p.Leu135Phe | missense_variant | 7/21 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000311 AC: 78AN: 251050Hom.: 2 AF XY: 0.000214 AC XY: 29AN XY: 135686
GnomAD4 exome AF: 0.0000712 AC: 104AN: 1461614Hom.: 9 Cov.: 30 AF XY: 0.0000523 AC XY: 38AN XY: 727094
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2022 | The c.403C>T (p.L135F) alteration is located in exon 7 (coding exon 5) of the SLC37A1 gene. This alteration results from a C to T substitution at nucleotide position 403, causing the leucine (L) at amino acid position 135 to be replaced by a phenylalanine (F). 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