rs12373788
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000416668.5(FTCDNL1):c.212-8057C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,148 control chromosomes in the GnomAD database, including 1,561 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 0.12 ( 1561 hom., cov: 32)
Consequence
FTCDNL1
ENST00000416668.5 intron
ENST00000416668.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.138
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=-0.94).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FTCDNL1 | NM_001350854.2 | c.*20-8057C>T | intron_variant | ||||
FTCDNL1 | NM_001350855.2 | c.212-8057C>T | intron_variant | ||||
FTCDNL1 | XM_024452852.2 | c.397+50680C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTCDNL1 | ENST00000416668.5 | c.212-8057C>T | intron_variant | 1 | |||||
FTCDNL1 | ENST00000420922.6 | c.*20-8057C>T | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.124 AC: 18903AN: 152030Hom.: 1562 Cov.: 32
GnomAD3 genomes
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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: 0.124 AC: 18895AN: 152148Hom.: 1561 Cov.: 32 AF XY: 0.129 AC XY: 9559AN XY: 74352
GnomAD4 genome
?
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18895
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152148
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32
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9559
AN XY:
74352
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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