chr10-100916720-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018121.4(SLF2):c.335T>C(p.Ile112Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000153 in 1,569,108 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.335T>C | p.Ile112Thr | missense_variant | 3/20 | ENST00000238961.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF2 | ENST00000238961.9 | c.335T>C | p.Ile112Thr | missense_variant | 3/20 | 1 | NM_018121.4 | P2 | |
SLF2 | ENST00000370269.3 | c.335T>C | p.Ile112Thr | missense_variant | 3/19 | 1 | A2 | ||
SLF2 | ENST00000370271.7 | c.335T>C | p.Ile112Thr | missense_variant | 3/6 | 1 | |||
SLF2 | ENST00000649226.1 | c.335T>C | p.Ile112Thr | missense_variant, NMD_transcript_variant | 3/21 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000188 AC: 4AN: 212818Hom.: 0 AF XY: 0.0000262 AC XY: 3AN XY: 114520
GnomAD4 exome AF: 0.0000148 AC: 21AN: 1416982Hom.: 0 Cov.: 31 AF XY: 0.0000228 AC XY: 16AN XY: 702182
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | The c.335T>C (p.I112T) alteration is located in exon 3 (coding exon 3) of the SLF2 gene. This alteration results from a T to C substitution at nucleotide position 335, causing the isoleucine (I) at amino acid position 112 to be replaced by a threonine (T). 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