17-7482013-C-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.29C>T(p.Pro10Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,605,496 control chromosomes in the GnomAD database, including 1 homozygotes. 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 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC35G6 | NM_001102614.2 | c.29C>T | p.Pro10Leu | missense_variant | Exon 2 of 2 | ENST00000412468.4 | NP_001096084.1 | |
SLC35G6 | XM_047436533.1 | c.35C>T | p.Pro12Leu | missense_variant | Exon 2 of 2 | XP_047292489.1 | ||
ZBTB4 | NM_020899.4 | c.-81+1991G>A | intron_variant | Intron 1 of 3 | NP_065950.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 246208Hom.: 0 AF XY: 0.0000301 AC XY: 4AN XY: 133056
GnomAD4 exome AF: 0.0000227 AC: 33AN: 1453202Hom.: 0 Cov.: 32 AF XY: 0.0000263 AC XY: 19AN XY: 722018
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152294Hom.: 1 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:1
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