chr15-56894199-A-G

Position:

• chr15-56894199-A-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.1109-4032T>C 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 0.377 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: TCF12-DT NR_015419.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCF12-DT	NR_015419.2	n.1109-4032T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCF12-DT	ENST00000648603.1	n.1113-4032T>C		intron_variant, non_coding_transcript_variant
TCF12-DT	ENST00000559920.5	n.258-4032T>C		intron_variant, non_coding_transcript_variant		2
TCF12-DT	ENST00000561122.1	n.1109-4032T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.353

Alfa AF: 0.254 Hom.: 2993

Bravo AF: 0.399

Asia WGS AF: 0.382 AC: 1330 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	15
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7175191; hg19: chr15-57186397;