chr17-7482402-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001102614.2(SLC35G6):c.418G>A(p.Val140Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,613,990 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V140G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001102614.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35G6 | NM_001102614.2 | c.418G>A | p.Val140Ile | missense_variant | 2/2 | ENST00000412468.4 | |
SLC35G6 | XM_047436533.1 | c.424G>A | p.Val142Ile | missense_variant | 2/2 | ||
ZBTB4 | NM_020899.4 | c.-81+1602C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35G6 | ENST00000412468.4 | c.418G>A | p.Val140Ile | missense_variant | 2/2 | 1 | NM_001102614.2 | P1 | |
ZBTB4 | ENST00000311403.4 | c.-81+1602C>T | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251184Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135742
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461664Hom.: 0 Cov.: 122 AF XY: 0.00000825 AC XY: 6AN XY: 727144
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | The c.418G>A (p.V140I) alteration is located in exon 2 (coding exon 2) of the SLC35G6 gene. This alteration results from a G to A substitution at nucleotide position 418, causing the valine (V) at amino acid position 140 to be replaced by an isoleucine (I). 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