ENST00000559000.6:c.-703+7588A>T

Variant names:

• chr15-56909559-T-A
• rs1975092
• ENST00000559000.6:c.-703+7588A>T

Variant summary

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

The ENST00000559000.6(ENSG00000285253):​c.-703+7588A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 151,864 control chromosomes in the GnomAD database, including 39,022 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 0.71 (39022 hom., cov: 29)
• Consequence: ENSG00000285253 ENST00000559000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCF12-DT	NR_015419.2	n.1108+7506A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285253	ENST00000559000.6	c.-703+7588A>T		intron_variant	Intron 2 of 23	2		ENSP00000453045.1
TCF12-DT	ENST00000559920.5	n.257+7506A>T		intron_variant	Intron 2 of 3	2
TCF12-DT	ENST00000561122.1	n.1108+7506A>T		intron_variant	Intron 2 of 3	2
TCF12-DT	ENST00000648603.1	n.995-3694A>T		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108318 AN: 151744 Hom.: 38996 Cov.: 29

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.714 AC: 108393 AN: 151864 Hom.: 39022 Cov.: 29 AF XY: 0.714 AC XY: 53007 AN XY: 74204

African (AFR) AF: 0.650 AC: 26899 AN: 41394

American (AMR) AF: 0.741 AC: 11308 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2749 AN: 3470

East Asian (EAS) AF: 0.504 AC: 2602 AN: 5162

South Asian (SAS) AF: 0.729 AC: 3501 AN: 4800

European-Finnish (FIN) AF: 0.744 AC: 7834 AN: 10524

Middle Eastern (MID) AF: 0.745 AC: 216 AN: 290

European-Non Finnish (NFE) AF: 0.751 AC: 51047 AN: 67934

Other (OTH) AF: 0.714 AC: 1505 AN: 2108

Alfa AF: 0.733 Hom.: 5146

Bravo AF: 0.710

Asia WGS AF: 0.642 AC: 2229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.70
PhyloP100		0.61
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1975092; hg19: chr15-57201757;