chr6-133889838-G-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003206.4(TCF21):c.441G>T(p.Pro147=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00209 in 1,612,738 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0017 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 6 hom. )
Consequence
TCF21
NM_003206.4 synonymous
NM_003206.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.22
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 6-133889838-G-T is Benign according to our data. Variant chr6-133889838-G-T is described in ClinVar as [Benign]. Clinvar id is 731660.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.22 with no splicing effect.
BS2
?
High AC in GnomAd at 255 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCF21 | NM_003206.4 | c.441G>T | p.Pro147= | synonymous_variant | 1/2 | ENST00000367882.5 | |
TCF21 | NM_198392.3 | c.441G>T | p.Pro147= | synonymous_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF21 | ENST00000367882.5 | c.441G>T | p.Pro147= | synonymous_variant | 1/2 | 1 | NM_003206.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00168 AC: 255AN: 152178Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00160 AC: 395AN: 246130Hom.: 0 AF XY: 0.00174 AC XY: 234AN XY: 134286
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GnomAD4 exome AF: 0.00213 AC: 3113AN: 1460442Hom.: 6 Cov.: 34 AF XY: 0.00211 AC XY: 1535AN XY: 726520
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GnomAD4 genome ? AF: 0.00167 AC: 255AN: 152296Hom.: 1 Cov.: 32 AF XY: 0.00171 AC XY: 127AN XY: 74466
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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 07, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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