rs13334205

Variant names:

• chr16-67547980-A-G
• rs13334205
• ENST00000748474.1:n.183+15315T>C

Variant summary

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

The ENST00000748474.1(CTCF-DT):​n.183+15315T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,244 control chromosomes in the GnomAD database, including 10,385 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 0.28 (10385 hom., cov: 33)
• Consequence: CTCF-DT ENST00000748474.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• Publications: 15 publications found

Genes affected

CTCF-DT (HGNC:55409): (CTCF divergent transcript)

ENSG00000297582 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTCF-DT	ENST00000748474.1	n.183+15315T>C		intron_variant	Intron 1 of 1
ENSG00000297582	ENST00000749076.1	n.-75T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42304 AN: 152126 Hom.: 10344 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.278 AC: 42398 AN: 152244 Hom.: 10385 Cov.: 33 AF XY: 0.274 AC XY: 20363 AN XY: 74432

African (AFR) AF: 0.664 AC: 27571 AN: 41518

American (AMR) AF: 0.152 AC: 2327 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3470

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5176

South Asian (SAS) AF: 0.191 AC: 920 AN: 4824

European-Finnish (FIN) AF: 0.164 AC: 1742 AN: 10618

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8767 AN: 68010

Other (OTH) AF: 0.227 AC: 481 AN: 2116

Alfa AF: 0.172 Hom.: 9735

Bravo AF: 0.290

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	19
DANN	Benign	0.71
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs13334205; hg19: chr16-67581883;