17-7482576-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001102614.2(SLC35G6):c.592G>T(p.Val198Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000837 in 1,612,222 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001102614.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35G6 | NM_001102614.2 | c.592G>T | p.Val198Leu | missense_variant | 2/2 | ENST00000412468.4 | |
SLC35G6 | XM_047436533.1 | c.598G>T | p.Val200Leu | missense_variant | 2/2 | ||
ZBTB4 | NM_020899.4 | c.-81+1428C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35G6 | ENST00000412468.4 | c.592G>T | p.Val198Leu | missense_variant | 2/2 | 1 | NM_001102614.2 | P1 | |
ZBTB4 | ENST00000311403.4 | c.-81+1428C>A | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251312Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135816
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1460042Hom.: 0 Cov.: 129 AF XY: 0.0000688 AC XY: 50AN XY: 726318
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74340
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at