17-35548717-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001129820.2(SLFN14):c.2261C>T(p.Pro754Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,216 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_001129820.2 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 |
---|---|---|---|---|---|---|---|
SLFN14 | NM_001129820.2 | c.2261C>T | p.Pro754Leu | missense_variant | 6/6 | ENST00000674182.1 | |
SLFN14 | XM_017024577.2 | c.2261C>T | p.Pro754Leu | missense_variant | 6/6 | ||
SLFN14 | XM_017024578.2 | c.2261C>T | p.Pro754Leu | missense_variant | 5/5 | ||
SLFN14 | XM_017024579.2 | c.2261C>T | p.Pro754Leu | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLFN14 | ENST00000674182.1 | c.2261C>T | p.Pro754Leu | missense_variant | 6/6 | NM_001129820.2 | P1 | ||
SLFN14 | ENST00000415846.3 | c.2261C>T | p.Pro754Leu | missense_variant | 4/4 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1399384Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 690198
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.2261C>T (p.P754L) alteration is located in exon 4 (coding exon 4) of the SLFN14 gene. This alteration results from a C to T substitution at nucleotide position 2261, causing the proline (P) at amino acid position 754 to be replaced by a leucine (L). 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