rs9909601
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001363830.2(SLFN12L):c.87-10208T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLFN12L
NM_001363830.2 intron
NM_001363830.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.52
Genes affected
SLFN12L (HGNC:33920): (schlafen family member 12 like) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLFN12L | NM_001363830.2 | c.87-10208T>G | intron_variant | ENST00000628453.4 | |||
SLFN12L | NM_001195790.3 | c.-287-2431T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLFN12L | ENST00000628453.4 | c.87-10208T>G | intron_variant | 5 | NM_001363830.2 | A2 | |||
E2F3P1 | ENST00000589887.1 | n.395A>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1104070Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 564204
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1104070
Hom.:
Cov.:
22
AF XY:
AC XY:
0
AN XY:
564204
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at