6-87472981-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_ModerateBP6_Very_Strong
The NM_006416.5(SLC35A1):c.-23C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 659,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006416.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC35A1 | NM_006416.5 | c.-23C>T | 5_prime_UTR_variant | Exon 1 of 8 | ENST00000369552.9 | NP_006407.1 | ||
SLC35A1 | NM_001168398.2 | c.-23C>T | 5_prime_UTR_variant | Exon 1 of 7 | NP_001161870.1 | |||
LOC124901357 | XR_007059668.1 | n.-36G>A | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152196Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.000110 AC: 56AN: 507208Hom.: 0 Cov.: 6 AF XY: 0.000141 AC XY: 37AN XY: 263222
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152314Hom.: 0 Cov.: 34 AF XY: 0.0000940 AC XY: 7AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at