chr6-133889667-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_003206.4(TCF21):c.270C>T(p.Ala90=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00872 in 1,613,866 control chromosomes in the GnomAD database, including 108 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0075 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0089 ( 99 hom. )
Consequence
TCF21
NM_003206.4 synonymous
NM_003206.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.668
Genes affected
TCF21 (HGNC:11632): (transcription factor 21) TCF21 encodes a transcription factor of the basic helix-loop-helix family. The TCF21 product is mesoderm specific, and expressed in embryonic epicardium, mesenchyme-derived tissues of lung, gut, gonad, and both mesenchymal and glomerular epithelial cells in the kidney. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 6-133889667-C-T is Benign according to our data. Variant chr6-133889667-C-T is described in ClinVar as [Benign]. Clinvar id is 769693.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.668 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.00885 (12936/1461660) while in subpopulation SAS AF= 0.016 (1380/86254). AF 95% confidence interval is 0.0153. There are 99 homozygotes in gnomad4_exome. There are 6684 alleles in male gnomad4_exome subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1144 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCF21 | NM_003206.4 | c.270C>T | p.Ala90= | synonymous_variant | 1/2 | ENST00000367882.5 | |
TCF21 | NM_198392.3 | c.270C>T | p.Ala90= | synonymous_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF21 | ENST00000367882.5 | c.270C>T | p.Ala90= | synonymous_variant | 1/2 | 1 | NM_003206.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00750 AC: 1140AN: 152086Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00878 AC: 2201AN: 250802Hom.: 19 AF XY: 0.00904 AC XY: 1228AN XY: 135776
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GnomAD4 exome AF: 0.00885 AC: 12936AN: 1461660Hom.: 99 Cov.: 34 AF XY: 0.00919 AC XY: 6684AN XY: 727150
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GnomAD4 genome AF: 0.00752 AC: 1144AN: 152206Hom.: 9 Cov.: 32 AF XY: 0.00742 AC XY: 552AN XY: 74424
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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 | Jul 12, 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