rs782308530
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 6P and 2B. PM1PM2PM5BP4BP6
The ENST00000330775.9(SLC37A4):āc.80A>Gā(p.Asn27Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000867 in 1,613,908 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N27K) has been classified as Likely pathogenic.
Frequency
Consequence
ENST00000330775.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC37A4 | NM_001164277.2 | c.80A>G | p.Asn27Ser | missense_variant | 3/11 | ENST00000642844.3 | |
SLC37A4 | NM_001164279.2 | c.-172+102A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC37A4 | ENST00000330775.9 | c.80A>G | p.Asn27Ser | missense_variant | 2/10 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152216Hom.: 1 Cov.: 33
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461574Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727060
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152334Hom.: 1 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74506
ClinVar
Submissions by phenotype
Glucose-6-phosphate transport defect Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jul 19, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at