rs6674171
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_182499.4(TDRD10):c.142-1097A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,232 control chromosomes in the GnomAD database, including 3,059 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 0.19 ( 3059 hom., cov: 33)
Consequence
TDRD10
NM_182499.4 intron
NM_182499.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0620
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=-0.56).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TDRD10 | NM_182499.4 | c.142-1097A>G | intron_variant | ENST00000368482.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TDRD10 | ENST00000368482.8 | c.142-1097A>G | intron_variant | 1 | NM_182499.4 | P1 | |||
TDRD10 | ENST00000368480.3 | c.142-1097A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.192 AC: 29211AN: 152114Hom.: 3053 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: 0.192 AC: 29246AN: 152232Hom.: 3059 Cov.: 33 AF XY: 0.199 AC XY: 14788AN XY: 74426
GnomAD4 genome
?
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29246
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152232
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33
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14788
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74426
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775
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3474
ClinVar
Not reported inComputational scores
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Name
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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