NM_006006.6:c.1453+15115C>T

Variant names:

• chr11-114202153-C-T
• rs3782000
• NM_006006.6:c.1453+15115C>T

Variant summary

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

The NM_006006.6(ZBTB16):​c.1453+15115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,040 control chromosomes in the GnomAD database, including 2,997 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 0.18 (2997 hom., cov: 32)
• Consequence: ZBTB16 NM_006006.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

Genes affected

ZBTB16 (HGNC:12930): (zinc finger and BTB domain containing 16) This gene is a member of the Krueppel C2H2-type zinc-finger protein family and encodes a zinc finger transcription factor that contains nine Kruppel-type zinc finger domains at the carboxyl terminus. This protein is located in the nucleus, is involved in cell cycle progression, and interacts with a histone deacetylase. Specific instances of aberrant gene rearrangement at this locus have been associated with acute promyelocytic leukemia (APL). Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB16	NM_006006.6	c.1453+15115C>T		intron_variant	Intron 4 of 6	ENST00000335953.9	NP_005997.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB16	ENST00000335953.9	c.1453+15115C>T		intron_variant	Intron 4 of 6	1	NM_006006.6	ENSP00000338157.4

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27966 AN: 151924 Hom.: 2999 Cov.: 32

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.184 AC: 27945 AN: 152040 Hom.: 2997 Cov.: 32 AF XY: 0.179 AC XY: 13326 AN XY: 74300

Gnomad4 AFR AF: 0.0936

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.232

Alfa AF: 0.232 Hom.: 8770

Bravo AF: 0.185

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3782000; hg19: chr11-114072875;