chr21-42539566-C-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001320537.2(SLC37A1):āc.405C>Gā(p.Leu135=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000923 in 1,613,972 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Synonymous variant affecting the same amino acid position (i.e. L135L) has been classified as Benign.
Frequency
Consequence
NM_001320537.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC37A1 | NM_001320537.2 | c.405C>G | p.Leu135= | synonymous_variant | 6/20 | ENST00000352133.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC37A1 | ENST00000352133.3 | c.405C>G | p.Leu135= | synonymous_variant | 6/20 | 1 | NM_001320537.2 | P1 | |
SLC37A1 | ENST00000398341.7 | c.405C>G | p.Leu135= | synonymous_variant | 7/21 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00453 AC: 689AN: 152220Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00110 AC: 277AN: 251096Hom.: 6 AF XY: 0.000811 AC XY: 110AN XY: 135700
GnomAD4 exome AF: 0.000545 AC: 796AN: 1461634Hom.: 10 Cov.: 30 AF XY: 0.000473 AC XY: 344AN XY: 727114
GnomAD4 genome AF: 0.00456 AC: 694AN: 152338Hom.: 6 Cov.: 33 AF XY: 0.00428 AC XY: 319AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at