ENST00000559000.6:c.-702-4032T>C

Variant names:

• chr15-56894199-A-G
• rs7175191
• ENST00000559000.6:c.-702-4032T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000559000.6(ENSG00000285253):​c.-702-4032T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,084 control chromosomes in the GnomAD database, including 15,545 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 0.38 (15545 hom., cov: 32)
• Consequence: ENSG00000285253 ENST00000559000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648
• Publications: 3 publications found

Genes affected

ENSG00000285253 (HGNC:):

TCF12-DT (HGNC:27078): (TCF12 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559000.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCF12-DT	NR_015419.2		n.1109-4032T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285253	ENST00000559000.6	TSL:2	c.-702-4032T>C		intron	N/A	ENSP00000453045.1	H0YL38
	TCF12-DT	ENST00000559920.5	TSL:2	n.258-4032T>C		intron	N/A
	TCF12-DT	ENST00000561122.1	TSL:2	n.1109-4032T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57286 AN: 151966 Hom.: 15507 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.377 AC: 57363 AN: 152084 Hom.: 15545 Cov.: 32 AF XY: 0.375 AC XY: 27880 AN XY: 74332

African (AFR) AF: 0.767 AC: 31808 AN: 41462

American (AMR) AF: 0.250 AC: 3818 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2249 AN: 5174

South Asian (SAS) AF: 0.333 AC: 1602 AN: 4812

European-Finnish (FIN) AF: 0.177 AC: 1870 AN: 10586

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13639 AN: 67968

Other (OTH) AF: 0.353 AC: 746 AN: 2114

Alfa AF: 0.251 Hom.: 3239

Bravo AF: 0.399

Asia WGS AF: 0.382 AC: 1330 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	15
DANN	Benign	0.61
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7175191;

hg19: chr15-57186397;