rs2084414
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001384899.1(TDRP):c.108+2915C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,050 control chromosomes in the GnomAD database, including 42,990 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 0.75 ( 42990 hom., cov: 32)
Consequence
TDRP
NM_001384899.1 intron
NM_001384899.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0270
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=-0.98).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TDRP | NM_001384899.1 | c.108+2915C>T | intron_variant | ENST00000324079.11 | |||
TDRP | XM_047421392.1 | c.-26523C>T | 5_prime_UTR_variant | 2/4 | |||
TDRP | NM_001256113.2 | c.108+2915C>T | intron_variant | ||||
TDRP | NM_175075.5 | c.108+2915C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TDRP | ENST00000324079.11 | c.108+2915C>T | intron_variant | 1 | NM_001384899.1 | P1 | |||
TDRP | ENST00000523656.5 | c.108+2915C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.750 AC: 113905AN: 151932Hom.: 42933 Cov.: 32
GnomAD3 genomes
?
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113905
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151932
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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: 0.750 AC: 114024AN: 152050Hom.: 42990 Cov.: 32 AF XY: 0.742 AC XY: 55138AN XY: 74326
GnomAD4 genome
?
AF:
AC:
114024
AN:
152050
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32
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55138
AN XY:
74326
Gnomad4 AFR
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Asia WGS
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2704
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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