22-30636491-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001479.4(SLC35E4):c.41C>T(p.Thr14Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000785 in 1,528,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001479.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35E4 | NM_001001479.4 | c.41C>T | p.Thr14Ile | missense_variant | 1/2 | ENST00000343605.5 | |
SLC35E4 | NM_001318370.2 | c.41C>T | p.Thr14Ile | missense_variant | 1/3 | ||
SLC35E4 | NM_001318371.2 | c.41C>T | p.Thr14Ile | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35E4 | ENST00000343605.5 | c.41C>T | p.Thr14Ile | missense_variant | 1/2 | 1 | NM_001001479.4 | P1 | |
SLC35E4 | ENST00000406566.1 | c.41C>T | p.Thr14Ile | missense_variant | 1/3 | 1 | |||
SLC35E4 | ENST00000451479.1 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000694 AC: 1AN: 144086Hom.: 0 AF XY: 0.0000130 AC XY: 1AN XY: 76948
GnomAD4 exome AF: 0.00000363 AC: 5AN: 1376228Hom.: 0 Cov.: 30 AF XY: 0.00000444 AC XY: 3AN XY: 675214
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 15, 2024 | The c.41C>T (p.T14I) alteration is located in exon 1 (coding exon 1) of the SLC35E4 gene. This alteration results from a C to T substitution at nucleotide position 41, causing the threonine (T) at amino acid position 14 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at