rs12615435
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000416668.5(FTCDNL1):c.212-12951A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 152,282 control chromosomes in the GnomAD database, including 551 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 0.076 ( 551 hom., cov: 32)
Consequence
FTCDNL1
ENST00000416668.5 intron
ENST00000416668.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.823
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 (EAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FTCDNL1 | NM_001350854.2 | c.*20-12951A>C | intron_variant | ||||
FTCDNL1 | NM_001350855.2 | c.212-12951A>C | intron_variant | ||||
FTCDNL1 | XM_024452852.2 | c.397+45786A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTCDNL1 | ENST00000416668.5 | c.212-12951A>C | intron_variant | 1 | |||||
FTCDNL1 | ENST00000420922.6 | c.*20-12951A>C | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0754 AC: 11474AN: 152164Hom.: 544 Cov.: 32
GnomAD3 genomes
?
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11474
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152164
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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: 0.0755 AC: 11504AN: 152282Hom.: 551 Cov.: 32 AF XY: 0.0756 AC XY: 5631AN XY: 74454
GnomAD4 genome
?
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AC:
11504
AN:
152282
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32
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5631
AN XY:
74454
Gnomad4 AFR
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Asia WGS
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382
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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
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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