11-114190504-G-T

Position:

• chr11-114190504-G-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+3466G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,940 control chromosomes in the GnomAD database, including 5,771 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 0.25 (5771 hom., cov: 32)
• Consequence: ZBTB16 NM_006006.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB16	NM_006006.6	c.1453+3466G>T		intron_variant		ENST00000335953.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB16	ENST00000335953.9	c.1453+3466G>T		intron_variant		1	NM_006006.6	P1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37461 AN: 151820 Hom.: 5746 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.247 AC: 37533 AN: 151940 Hom.: 5771 Cov.: 32 AF XY: 0.245 AC XY: 18194 AN XY: 74254

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.251

Alfa AF: 0.168 Hom.: 3227

Bravo AF: 0.261

Asia WGS AF: 0.161 AC: 560 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.45

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: rs620095; hg19: chr11-114061226; COSMIC: COSV60098960; COSMIC: COSV60098960;