chr14-57589438-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001306087.2(SLC35F4):c.365C>A(p.Thr122Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000558 in 1,613,786 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T122M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001306087.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35F4 | NM_001306087.2 | c.365C>A | p.Thr122Lys | missense_variant | 3/8 | ENST00000556826.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35F4 | ENST00000556826.6 | c.365C>A | p.Thr122Lys | missense_variant | 3/8 | 5 | NM_001306087.2 | P1 | |
ENST00000647916.1 | n.872+7923G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248764Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134988
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461596Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727068
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 20, 2023 | The c.362C>A (p.T121K) alteration is located in exon 3 (coding exon 3) of the SLC35F4 gene. This alteration results from a C to A substitution at nucleotide position 362, causing the threonine (T) at amino acid position 121 to be replaced by a lysine (K). 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