chr10-100916632-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018121.4(SLF2):c.247A>G(p.Ile83Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000674 in 1,482,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLF2 | NM_018121.4 | c.247A>G | p.Ile83Val | missense_variant | 3/20 | ENST00000238961.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF2 | ENST00000238961.9 | c.247A>G | p.Ile83Val | missense_variant | 3/20 | 1 | NM_018121.4 | P2 | |
SLF2 | ENST00000370269.3 | c.247A>G | p.Ile83Val | missense_variant | 3/19 | 1 | A2 | ||
SLF2 | ENST00000370271.7 | c.247A>G | p.Ile83Val | missense_variant | 3/6 | 1 | |||
SLF2 | ENST00000649226.1 | c.247A>G | p.Ile83Val | missense_variant, NMD_transcript_variant | 3/21 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000601 AC: 8AN: 1330574Hom.: 0 Cov.: 30 AF XY: 0.00000615 AC XY: 4AN XY: 649972
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.247A>G (p.I83V) alteration is located in exon 3 (coding exon 3) of the SLF2 gene. This alteration results from a A to G substitution at nucleotide position 247, causing the isoleucine (I) at amino acid position 83 to be replaced by a valine (V). 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