rs2260722
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017905.6(TMCO3):c.1344-69A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 1,217,590 control chromosomes in the GnomAD database, including 63,354 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 0.40 ( 13815 hom., cov: 33)
Exomes 𝑓: 0.29 ( 49539 hom. )
Consequence
TMCO3
NM_017905.6 intron
NM_017905.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.16
Genes affected
TMCO3 (HGNC:20329): (transmembrane and coiled-coil domains 3) This gene encodes a member of the monovalent cation:proton antiporter 2 (CPA2) family of transporter proteins. Members of this family typically couple the export of monovalent cations, such as potassium or sodium, to the import of protons across cellular membranes. Mutations in this gene have been identified in patients with a rare inherited vision defect, cornea guttata with anterior polar cataract. [provided by RefSeq, Mar 2017]
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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 (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMCO3 | NM_017905.6 | c.1344-69A>G | intron_variant | ENST00000434316.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMCO3 | ENST00000434316.7 | c.1344-69A>G | intron_variant | 1 | NM_017905.6 | P1 | |||
TMCO3 | ENST00000375391.5 | c.1226-15658A>G | intron_variant | 1 | |||||
TMCO3 | ENST00000474393.5 | c.1344-69A>G | intron_variant | 2 | |||||
TMCO3 | ENST00000465556.1 | n.189-5381A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.395 AC: 60111AN: 152028Hom.: 13799 Cov.: 33
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GnomAD4 exome AF: 0.294 AC: 313454AN: 1065444Hom.: 49539 AF XY: 0.292 AC XY: 157369AN XY: 538024
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GnomAD4 genome ? AF: 0.396 AC: 60175AN: 152146Hom.: 13815 Cov.: 33 AF XY: 0.391 AC XY: 29121AN XY: 74388
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ClinVar
Not reported inComputational scores
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Name
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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