chr17-35259436-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144975.4(SLFN5):c.746C>T(p.Thr249Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000301 in 1,461,890 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Synonymous variant affecting the same amino acid position (i.e. T249T) has been classified as Likely benign.
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.746C>T | p.Thr249Met | missense_variant | 2/5 | ENST00000299977.9 | |
SLFN5 | NM_001330183.2 | c.746C>T | p.Thr249Met | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLFN5 | ENST00000299977.9 | c.746C>T | p.Thr249Met | missense_variant | 2/5 | 1 | NM_144975.4 | P1 | |
SLFN5 | ENST00000592325.1 | c.746C>T | p.Thr249Met | missense_variant | 2/2 | 1 | |||
SLFN5 | ENST00000542451.1 | c.746C>T | p.Thr249Met | missense_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251356Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135836
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727244
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.746C>T (p.T249M) alteration is located in exon 2 (coding exon 1) of the SLFN5 gene. This alteration results from a C to T substitution at nucleotide position 746, causing the threonine (T) at amino acid position 249 to be replaced by a methionine (M). 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