6-87472983-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_006416.5(SLC35A1):c.-21G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000781 in 665,816 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC35A1 | NM_006416.5 | c.-21G>A | 5_prime_UTR_variant | Exon 1 of 8 | ENST00000369552.9 | NP_006407.1 | ||
SLC35A1 | NM_001168398.2 | c.-21G>A | 5_prime_UTR_variant | Exon 1 of 7 | NP_001161870.1 | |||
LOC124901357 | XR_007059668.1 | n.-38C>T | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000155 AC: 2AN: 12918Hom.: 0 AF XY: 0.000309 AC XY: 2AN XY: 6472
GnomAD4 exome AF: 0.0000954 AC: 49AN: 513592Hom.: 1 Cov.: 7 AF XY: 0.0000601 AC XY: 16AN XY: 266114
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74362
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at