rs9916629
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001363830.2(SLFN12L):c.*5682A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 147,414 control chromosomes in the GnomAD database, including 7,351 homozygotes. 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: 𝑓 0.31 ( 7351 hom., cov: 23)
Consequence
SLFN12L
NM_001363830.2 3_prime_UTR
NM_001363830.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.118
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLFN12L | NM_001363830.2 | c.*5682A>G | 3_prime_UTR_variant | 5/5 | ENST00000628453.4 | ||
SLFN12L | NM_001195790.3 | c.*5682A>G | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLFN12L | ENST00000628453.4 | c.*5682A>G | 3_prime_UTR_variant | 5/5 | 5 | NM_001363830.2 | A2 | ||
SLFN12L | ENST00000260908.13 | c.*5682A>G | 3_prime_UTR_variant | 4/4 | 5 | P2 | |||
SLFN12L | ENST00000587436.1 | n.396-4579A>G | intron_variant, non_coding_transcript_variant | 2 | |||||
SLFN12L | ENST00000590802.1 | n.153-4660A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.311 AC: 45762AN: 147358Hom.: 7344 Cov.: 23
GnomAD3 genomes
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45762
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23
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.311 AC: 45778AN: 147414Hom.: 7351 Cov.: 23 AF XY: 0.303 AC XY: 21737AN XY: 71758
GnomAD4 genome
?
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45778
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23
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21737
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71758
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541
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at