chr22-37069345-C-CTGGGGTGGGGTGGGGTGGGGTGGGGTGGGGTGGGG
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_Strong
The NM_001374504.1(TMPRSS6):c.1842-2_1842-1insCCCCACCCCACCCCACCCCACCCCACCCCACCCCA variant causes a splice acceptor change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000022 ( 0 hom., cov: 0)
Consequence
TMPRSS6
NM_001374504.1 splice_acceptor
NM_001374504.1 splice_acceptor
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.94
Genes affected
TMPRSS6 (HGNC:16517): (transmembrane serine protease 6) The protein encoded by this gene is a type II transmembrane serine proteinase that is found attached to the cell surface. The encoded protein may be involved in matrix remodeling processes in the liver. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PVS1
?
Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.11249481 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.8, offset of 0 (no position change), new splice context is: cccaccccaccccaccccAGcat. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMPRSS6 | NM_001374504.1 | c.1842-2_1842-1insCCCCACCCCACCCCACCCCACCCCACCCCACCCCA | splice_acceptor_variant | ENST00000676104.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMPRSS6 | ENST00000676104.1 | c.1842-2_1842-1insCCCCACCCCACCCCACCCCACCCCACCCCACCCCA | splice_acceptor_variant | NM_001374504.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000220 AC: 2AN: 90956Hom.: 0 Cov.: 0
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GnomAD4 genome ? AF: 0.0000220 AC: 2AN: 90956Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 42994
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at