rs1975092

chr15-56909559-T-Achr15-56909559-T-Cchr15-56909559-T-G

Variant summary

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

The NR_015419.2(TCF12-DT):n.1108+7506A>T variant causes a intron, non coding transcript 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: TCF12-DT NR_015419.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TCF12-DT	NR_015419.2	n.1108+7506A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCF12-DT	ENST00000648603.1	n.995-3694A>T		intron_variant, non_coding_transcript_variant
TCF12-DT	ENST00000559920.5	n.257+7506A>T		intron_variant, non_coding_transcript_variant		2
TCF12-DT	ENST00000561122.1	n.1108+7506A>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.714

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1975092; hg19: chr15-57201757;