rs1364325599
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_005660.3(SLC35A2):c.275-10_275-8delTCC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000456 in 1,095,944 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005660.3 splice_region, intron
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC35A2 | NM_005660.3 | c.275-10_275-8delTCC | splice_region_variant, intron_variant | ENST00000247138.11 | NP_005651.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC35A2 | ENST00000247138.11 | c.275-10_275-8delTCC | splice_region_variant, intron_variant | 1 | NM_005660.3 | ENSP00000247138.5 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 0.00000456 AC: 5AN: 1095944Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 361362
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
SLC35A2-congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 20, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at