15-57050501-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207037.2(TCF12):c.149-13249A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,072 control chromosomes in the GnomAD database, including 51,760 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 0.82 (51760 hom., cov: 30)
• Consequence: TCF12 NM_207037.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCF12	NM_207037.2	c.149-13249A>G		intron_variant		ENST00000333725.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCF12	ENST00000333725.10	c.149-13249A>G		intron_variant		1	NM_207037.2	P4

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124707 AN: 151954 Hom.: 51703 Cov.: 30

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.811

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.821 AC: 124826 AN: 152072 Hom.: 51760 Cov.: 30 AF XY: 0.822 AC XY: 61063 AN XY: 74324

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.852

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.811

Alfa AF: 0.791 Hom.: 5606

Bravo AF: 0.829

Asia WGS AF: 0.824 AC: 2865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.75
Dann	Benign	0.47

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

Other links and lift over

dbSNP: rs2962994; hg19: chr15-57342699;