chr5-140634792-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_011537665.3(TMCO6):c.-129-6873C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 150,346 control chromosomes in the GnomAD database, including 31,665 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 ( 31665 hom., cov: 29)
Consequence
TMCO6
XM_011537665.3 intron
XM_011537665.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.34
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 (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMCO6 | XM_011537665.3 | c.-129-6873C>T | intron_variant | XP_011535967.1 | ||||
TMCO6 | XM_024446125.2 | c.-472-4947C>T | intron_variant | XP_024301893.1 | ||||
TMCO6 | XM_047417355.1 | c.-242-4947C>T | intron_variant | XP_047273311.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
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Frequencies
GnomAD3 genomes AF: 0.644 AC: 96796AN: 150224Hom.: 31602 Cov.: 29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.645 AC: 96919AN: 150346Hom.: 31665 Cov.: 29 AF XY: 0.644 AC XY: 47330AN XY: 73452
GnomAD4 genome
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47330
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at