rs13008446
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000416668.5(FTCDNL1):c.212-2942C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,196 control chromosomes in the GnomAD database, including 23,117 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 0.50 ( 23117 hom., cov: 33)
Consequence
FTCDNL1
ENST00000416668.5 intron
ENST00000416668.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0940
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 (NFE) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FTCDNL1 | NM_001350854.2 | c.*20-2942C>T | intron_variant | ||||
FTCDNL1 | NM_001350855.2 | c.212-2942C>T | intron_variant | ||||
FTCDNL1 | XM_024452852.2 | c.397+55795C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTCDNL1 | ENST00000416668.5 | c.212-2942C>T | intron_variant | 1 | |||||
FTCDNL1 | ENST00000420922.6 | c.*20-2942C>T | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.503 AC: 76562AN: 152078Hom.: 23118 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.503 AC: 76573AN: 152196Hom.: 23117 Cov.: 33 AF XY: 0.511 AC XY: 38052AN XY: 74422
GnomAD4 genome
?
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AC:
76573
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152196
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33
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38052
AN XY:
74422
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2000
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at