chr10-100924106-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018121.4(SLF2):c.1105C>T(p.His369Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018121.4 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
SLF2 | NM_018121.4 | c.1105C>T | p.His369Tyr | missense_variant | 5/20 | ENST00000238961.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF2 | ENST00000238961.9 | c.1105C>T | p.His369Tyr | missense_variant | 5/20 | 1 | NM_018121.4 | P2 | |
SLF2 | ENST00000370269.3 | c.1105C>T | p.His369Tyr | missense_variant | 5/19 | 1 | A2 | ||
SLF2 | ENST00000370271.7 | c.1105C>T | p.His369Tyr | missense_variant | 5/6 | 1 | |||
SLF2 | ENST00000649226.1 | c.1105C>T | p.His369Tyr | missense_variant, NMD_transcript_variant | 5/21 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250722Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135604
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461216Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726974
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The c.1105C>T (p.H369Y) alteration is located in exon 5 (coding exon 5) of the SLF2 gene. This alteration results from a C to T substitution at nucleotide position 1105, causing the histidine (H) at amino acid position 369 to be replaced by a tyrosine (Y). 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