Variant 15-57197836-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_207037.2(TCF12):c.579+11A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 1,612,982 control chromosomes in the GnomAD database, including 3,012 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.040 ( 376 hom., cov: 32)

Exomes 𝑓: 0.039 ( 2636 hom. )

Consequence

TCF12
NM_207037.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.540

Variant links:

Genes affected

TCF12 (HGNC:11623): (transcription factor 12) The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]

TCF12 links:

TCF12 (HGNC:):

TCF12 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 15-57197836-A-G is Benign according to our data. Variant chr15-57197836-A-G is described in ClinVar as [Benign]. Clinvar id is 263281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-57197836-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCF12	NM_207037.2 linkuse as main transcript	c.579+11A>G		intron_variant		ENST00000333725.10	NP_996920.1	Q99081-3A0A024R5Z0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCF12	ENST00000333725.10 linkuse as main transcript	c.579+11A>G		intron_variant		1	NM_207037.2	ENSP00000331057.6		Q99081-3

Frequencies

GnomAD3 genomes

AF:

0.0402

AC:

6121

AN:

152106

Hom.:

372

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0111

Gnomad AMI

AF:

0.0934

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.0289

Gnomad EAS

AF:

0.00250

Gnomad SAS

AF:

0.0284

Gnomad FIN

AF:

0.0324

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0344

Gnomad OTH

AF:

0.0483

GnomAD3 exomes

AF:

0.0632

AC:

15824

AN:

250378

Hom.:

1582

AF XY:

0.0542

AC XY:

7334

AN XY:

135282

show subpopulations

Gnomad AFR exome

AF:

0.00942

Gnomad AMR exome

AF:

0.273

Gnomad ASJ exome

AF:

0.0264

Gnomad EAS exome

AF:

0.00207

Gnomad SAS exome

AF:

0.0292

Gnomad FIN exome

AF:

0.0388

Gnomad NFE exome

AF:

0.0346

Gnomad OTH exome

AF:

0.0569

GnomAD4 exome

AF:

0.0391

AC:

57128

AN:

1460760

Hom.:

2636

Cov.:

AF XY:

0.0377

AC XY:

27396

AN XY:

726640

show subpopulations

Gnomad4 AFR exome

AF:

0.00742

Gnomad4 AMR exome

AF:

0.266

Gnomad4 ASJ exome

AF:

0.0268

Gnomad4 EAS exome

AF:

0.000958

Gnomad4 SAS exome

AF:

0.0303

Gnomad4 FIN exome

AF:

0.0407

Gnomad4 NFE exome

AF:

0.0335

Gnomad4 OTH exome

AF:

0.0366

GnomAD4 genome

AF:

0.0403

AC:

6137

AN:

152222

Hom.:

376

Cov.:

AF XY:

0.0419

AC XY:

3117

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0111

Gnomad4 AMR

AF:

0.168

Gnomad4 ASJ

AF:

0.0289

Gnomad4 EAS

AF:

0.00251

Gnomad4 SAS

AF:

0.0282

Gnomad4 FIN

AF:

0.0324

Gnomad4 NFE

AF:

0.0344

Gnomad4 OTH

AF:

0.0483

Alfa

AF:

0.0350

Hom.:

Bravo

AF:

0.0506

Asia WGS

AF:

0.0340

AC:

118

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.39

DANN

Benign

0.53

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over