5-140567663-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080670.4(SLC35A4):c.494G>A(p.Gly165Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080670.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35A4 | NM_080670.4 | c.494G>A | p.Gly165Glu | missense_variant | 3/3 | ENST00000323146.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35A4 | ENST00000323146.8 | c.494G>A | p.Gly165Glu | missense_variant | 3/3 | 1 | NM_080670.4 | P1 | |
SLC35A4 | ENST00000612662.2 | c.494G>A | p.Gly165Glu | missense_variant | 3/3 | 1 | P1 | ||
SLC35A4 | ENST00000514199.1 | c.494G>A | p.Gly165Glu | missense_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251144Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135794
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461734Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727172
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2022 | The c.494G>A (p.G165E) alteration is located in exon 3 (coding exon 1) of the SLC35A4 gene. This alteration results from a G to A substitution at nucleotide position 494, causing the glycine (G) at amino acid position 165 to be replaced by a glutamic acid (E). 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