12-88153276-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_181783.4(TMTC3):c.190-15G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000559 in 1,591,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000056 ( 0 hom. )
Consequence
TMTC3
NM_181783.4 splice_polypyrimidine_tract, intron
NM_181783.4 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0420
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 12-88153276-G-A is Benign according to our data. Variant chr12-88153276-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1534417.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMTC3 | NM_181783.4 | c.190-15G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000266712.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMTC3 | ENST00000266712.11 | c.190-15G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_181783.4 | P1 | |||
TMTC3 | ENST00000547034.5 | c.190-15G>A | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 1 | |||||
TMTC3 | ENST00000549011.5 | c.190-15G>A | splice_polypyrimidine_tract_variant, intron_variant | 4 | |||||
TMTC3 | ENST00000551088.1 | c.190-1012G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152018Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000377 AC: 9AN: 238842Hom.: 0 AF XY: 0.0000464 AC XY: 6AN XY: 129236
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GnomAD4 exome AF: 0.0000556 AC: 80AN: 1439452Hom.: 0 Cov.: 30 AF XY: 0.0000503 AC XY: 36AN XY: 715682
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GnomAD4 genome AF: 0.0000592 AC: 9AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74250
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 20, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at