dbSNP rs7766238: TCF21:c.*292A>G (chr6-133893438-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000237316.3(TCF21):c.*292A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,268 control chromosomes in the GnomAD database, including 61,467 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.90 ( 61449 hom., cov: 32)

Exomes 𝑓: 0.95 ( 18 hom. )

Consequence

TCF21
ENST00000237316.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

Publications

8 publications found

Variant links:

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]

TCF21 links:

TARID (HGNC:50506): (TCF21 antisense RNA inducing promoter demethylation)

TARID links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCF21	NM_198392.3 link	c.*292A>G		3_prime_UTR_variant	Exon 3 of 3		NP_938206.1	O43680

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
TCF21	ENST00000237316.3 link	c.*292A>G	3_prime_UTR_variant	Exon 3 of 3	1	ENSP00000237316.3	O43680
TARID	ENST00000795402.1 link	n.151+23624T>C	intron_variant	Intron 1 of 5
TARID	ENST00000795414.1 link	n.208+23624T>C	intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.898

AC:

136645

AN:

152110

Hom.:

61407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.868

Gnomad AMI

AF:

0.897

Gnomad AMR

AF:

0.943

Gnomad ASJ

AF:

0.885

Gnomad EAS

AF:

0.874

Gnomad SAS

AF:

0.906

Gnomad FIN

AF:

0.898

Gnomad MID

AF:

0.905

Gnomad NFE

AF:

0.909

Gnomad OTH

AF:

0.906

GnomAD4 exome

AF:

0.950

AC:

AN:

Hom.:

Cov.:

AF XY:

0.923

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.917

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.955

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.650

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.898

AC:

136739

AN:

152228

Hom.:

61449

Cov.:

AF XY:

0.899

AC XY:

66906

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.868

AC:

36034

AN:

41516

American (AMR)

AF:

0.943

AC:

14426

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.885

AC:

3072

AN:

3470

East Asian (EAS)

AF:

0.874

AC:

4515

AN:

5166

South Asian (SAS)

AF:

0.907

AC:

4379

AN:

4830

European-Finnish (FIN)

AF:

0.898

AC:

9529

AN:

10612

Middle Eastern (MID)

AF:

0.898

AC:

264

AN:

294

European-Non Finnish (NFE)

AF:

0.909

AC:

61792

AN:

68012

Other (OTH)

AF:

0.903

AC:

1910

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

724

1448

2172

2896

3620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

904

1808

2712

3616

4520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.901

Hom.:

20698

Bravo

AF:

0.903

Asia WGS

AF:

0.867

AC:

3015

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.20

(source)

DANN

Benign

0.50

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over