chr10-104002739-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014720.4(SLK):c.1561G>T(p.Gly521Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,461,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014720.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLK | NM_014720.4 | c.1561G>T | p.Gly521Trp | missense_variant | 9/19 | ENST00000369755.4 | |
SLK | NM_001304743.2 | c.1561G>T | p.Gly521Trp | missense_variant | 9/18 | ||
SLK | XM_011540401.4 | c.993+1167G>T | intron_variant | ||||
SLK | XM_047426039.1 | c.993+1167G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLK | ENST00000369755.4 | c.1561G>T | p.Gly521Trp | missense_variant | 9/19 | 1 | NM_014720.4 | P1 | |
SLK | ENST00000335753.8 | c.1561G>T | p.Gly521Trp | missense_variant | 9/18 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461490Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727046
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.1561G>T (p.G521W) alteration is located in exon 9 (coding exon 9) of the SLK gene. This alteration results from a G to T substitution at nucleotide position 1561, causing the glycine (G) at amino acid position 521 to be replaced by a tryptophan (W). 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