rs17116334

Positions:

• chr11-114091040-C-T

Variant summary

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

The ENST00000335953.9(ZBTB16):​c.1268+26472C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,112 control chromosomes in the GnomAD database, including 2,792 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 (2792 hom., cov: 32)
• Consequence: ZBTB16 ENST00000335953.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB16	NM_006006.6	c.1268+26472C>T		intron_variant		ENST00000335953.9	NP_005997.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB16	ENST00000335953.9	c.1268+26472C>T		intron_variant		1	NM_006006.6	ENSP00000338157	P1

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26924 AN: 151992 Hom.: 2792 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.177 AC: 26937 AN: 152112 Hom.: 2792 Cov.: 32 AF XY: 0.177 AC XY: 13126 AN XY: 74354

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.185

Alfa AF: 0.147 Hom.: 3188

Bravo AF: 0.178

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.60

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: rs17116334; hg19: chr11-113961762; COSMIC: COSV60098186;