12-29583398-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001193451.2(TMTC1):c.1418+9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,612,742 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0092 ( 18 hom., cov: 33)
Exomes 𝑓: 0.00089 ( 13 hom. )
Consequence
TMTC1
NM_001193451.2 intron
NM_001193451.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.21
Genes affected
TMTC1 (HGNC:24099): (transmembrane O-mannosyltransferase targeting cadherins 1) Enables mannosyltransferase activity. Involved in protein O-linked mannosylation. Predicted to be located in endoplasmic reticulum. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 12-29583398-T-C is Benign according to our data. Variant chr12-29583398-T-C is described in ClinVar as [Benign]. Clinvar id is 785397.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00916 (1396/152370) while in subpopulation AFR AF= 0.0318 (1322/41576). AF 95% confidence interval is 0.0304. There are 18 homozygotes in gnomad4. There are 666 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 18 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMTC1 | NM_001193451.2 | c.1418+9A>G | intron_variant | ENST00000539277.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMTC1 | ENST00000539277.6 | c.1418+9A>G | intron_variant | 1 | NM_001193451.2 |
Frequencies
GnomAD3 genomes AF: 0.00903 AC: 1375AN: 152252Hom.: 18 Cov.: 33
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GnomAD3 exomes AF: 0.00240 AC: 599AN: 249872Hom.: 12 AF XY: 0.00171 AC XY: 231AN XY: 135008
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GnomAD4 exome AF: 0.000887 AC: 1296AN: 1460372Hom.: 13 Cov.: 30 AF XY: 0.000789 AC XY: 573AN XY: 726444
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GnomAD4 genome AF: 0.00916 AC: 1396AN: 152370Hom.: 18 Cov.: 33 AF XY: 0.00894 AC XY: 666AN XY: 74528
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 14, 2018 | - - |
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