rs753345092
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001129820.2(SLFN14):āc.1358A>Gā(p.Asn453Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000967 in 1,551,530 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001129820.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLFN14 | NM_001129820.2 | c.1358A>G | p.Asn453Ser | missense_variant | 5/6 | ENST00000674182.1 | NP_001123292.1 | |
LOC107985033 | NR_138031.1 | n.72T>C | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLFN14 | ENST00000674182.1 | c.1358A>G | p.Asn453Ser | missense_variant | 5/6 | NM_001129820.2 | ENSP00000501524 | P1 | ||
SLFN14 | ENST00000415846.3 | c.1358A>G | p.Asn453Ser | missense_variant | 3/4 | 1 | ENSP00000391101 | P1 | ||
ENST00000588445.1 | n.72T>C | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152138Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000649 AC: 10AN: 153970Hom.: 0 AF XY: 0.0000367 AC XY: 3AN XY: 81690
GnomAD4 exome AF: 0.0000958 AC: 134AN: 1399392Hom.: 0 Cov.: 32 AF XY: 0.000101 AC XY: 70AN XY: 690204
GnomAD4 genome AF: 0.000105 AC: 16AN: 152138Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 06, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at