chr17-35259168-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144975.4(SLFN5):āc.478G>Cā(p.Gly160Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,614,076 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_144975.4 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 |
---|---|---|---|---|---|---|---|
SLFN5 | NM_144975.4 | c.478G>C | p.Gly160Arg | missense_variant | 2/5 | ENST00000299977.9 | |
SLFN5 | NM_001330183.2 | c.478G>C | p.Gly160Arg | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLFN5 | ENST00000299977.9 | c.478G>C | p.Gly160Arg | missense_variant | 2/5 | 1 | NM_144975.4 | P1 | |
SLFN5 | ENST00000592325.1 | c.478G>C | p.Gly160Arg | missense_variant | 2/2 | 1 | |||
SLFN5 | ENST00000542451.1 | c.478G>C | p.Gly160Arg | missense_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000679 AC: 17AN: 250354Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135384
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461820Hom.: 1 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 727206
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.478G>C (p.G160R) alteration is located in exon 2 (coding exon 1) of the SLFN5 gene. This alteration results from a G to C substitution at nucleotide position 478, causing the glycine (G) at amino acid position 160 to be replaced by an arginine (R). 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