6-87477487-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_006416.5(SLC35A1):c.142G>A(p.Val48Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,744 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 (★).
Frequency
Consequence
NM_006416.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC35A1 | ENST00000369552.9 | c.142G>A | p.Val48Met | missense_variant | Exon 2 of 8 | 1 | NM_006416.5 | ENSP00000358565.4 | ||
ENSG00000213204 | ENST00000507897.5 | n.*186G>A | non_coding_transcript_exon_variant | Exon 14 of 16 | 2 | ENSP00000426769.1 | ||||
ENSG00000213204 | ENST00000507897.5 | n.*186G>A | 3_prime_UTR_variant | Exon 14 of 16 | 2 | ENSP00000426769.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251448Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135902
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461744Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727168
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.142G>A (p.V48M) alteration is located in exon 2 (coding exon 2) of the SLC35A1 gene. This alteration results from a G to A substitution at nucleotide position 142, causing the valine (V) at amino acid position 48 to be replaced by a methionine (M). 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