rs7605378
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001363886.2(FTCDNL1):c.*502T>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 0.639 in 151,950 control chromosomes in the GnomAD database, including 31,231 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 0.64 ( 31231 hom., cov: 31)
Consequence
FTCDNL1
NM_001363886.2 3_prime_UTR
NM_001363886.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.101
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=-0.84).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FTCDNL1 | NM_001363886.2 | c.*502T>G | 3_prime_UTR_variant | 5/5 | ENST00000420128.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTCDNL1 | ENST00000420128.6 | c.*502T>G | 3_prime_UTR_variant | 5/5 | 5 | NM_001363886.2 | |||
FTCDNL1 | ENST00000416668.5 | c.211+33872T>G | intron_variant | 1 | |||||
FTCDNL1 | ENST00000420922.6 | c.*19+32177T>G | intron_variant | 5 | P1 | ||||
FTCDNL1 | ENST00000642693.1 | n.405+7369T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.639 AC: 96978AN: 151832Hom.: 31222 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.639 AC: 97030AN: 151950Hom.: 31231 Cov.: 31 AF XY: 0.637 AC XY: 47302AN XY: 74286
GnomAD4 genome
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97030
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151950
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31
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47302
AN XY:
74286
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2215
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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