rs2408296
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_102431.3(C13orf42):n.136+7221C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,016 control chromosomes in the GnomAD database, including 4,472 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 0.23 ( 4472 hom., cov: 32)
Consequence
C13orf42
NR_102431.3 intron, non_coding_transcript
NR_102431.3 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.61
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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C13orf42 | NR_102431.3 | n.136+7221C>T | intron_variant, non_coding_transcript_variant | ||||
C13orf42 | NR_102432.3 | n.235+6956C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C13orf42 | ENST00000433280.6 | n.136+7221C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
C13orf42 | ENST00000569306.1 | n.235+6956C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
C13orf42 | ENST00000636098.1 | n.206+35015C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.232 AC: 35262AN: 151896Hom.: 4467 Cov.: 32
GnomAD3 genomes
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35262
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.232 AC: 35266AN: 152016Hom.: 4472 Cov.: 32 AF XY: 0.232 AC XY: 17247AN XY: 74304
GnomAD4 genome
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152016
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32
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17247
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74304
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510
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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