chr17-35440898-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144682.6(SLFN13):āc.2391G>Cā(p.Arg797Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,613,996 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_144682.6 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 |
---|---|---|---|---|---|---|---|
SLFN13 | NM_144682.6 | c.2391G>C | p.Arg797Ser | missense_variant | 6/6 | ENST00000285013.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLFN13 | ENST00000285013.11 | c.2391G>C | p.Arg797Ser | missense_variant | 6/6 | 1 | NM_144682.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152184Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251396Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135868
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461812Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727210
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152184Hom.: 1 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.2391G>C (p.R797S) alteration is located in exon 6 (coding exon 4) of the SLFN13 gene. This alteration results from a G to C substitution at nucleotide position 2391, causing the arginine (R) at amino acid position 797 to be replaced by a serine (S). 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