17-7482260-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001102614.2(SLC35G6):c.276C>A(p.Asp92Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,926 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_001102614.2 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 |
---|---|---|---|---|---|---|---|
SLC35G6 | NM_001102614.2 | c.276C>A | p.Asp92Glu | missense_variant | 2/2 | ENST00000412468.4 | |
SLC35G6 | XM_047436533.1 | c.282C>A | p.Asp94Glu | missense_variant | 2/2 | ||
ZBTB4 | NM_020899.4 | c.-81+1744G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35G6 | ENST00000412468.4 | c.276C>A | p.Asp92Glu | missense_variant | 2/2 | 1 | NM_001102614.2 | P1 | |
ZBTB4 | ENST00000311403.4 | c.-81+1744G>T | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152254Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251182Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135744
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461672Hom.: 0 Cov.: 97 AF XY: 0.00000688 AC XY: 5AN XY: 727146
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2023 | The c.276C>A (p.D92E) alteration is located in exon 2 (coding exon 2) of the SLC35G6 gene. This alteration results from a C to A substitution at nucleotide position 276, causing the aspartic acid (D) at amino acid position 92 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