chr11-114254538-C-T

Position:

• chr11-114254538-C-T

Variant summary

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

The NM_006006.6(ZBTB16):​c.*3983C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,150 control chromosomes in the GnomAD database, including 1,836 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 0.14 (1836 hom., cov: 32)
• Consequence: ZBTB16 NM_006006.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB16	NM_006006.6	c.*3983C>T		3_prime_UTR_variant	7/7	ENST00000335953.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB16	ENST00000335953.9	c.*3983C>T		3_prime_UTR_variant	7/7	1	NM_006006.6	P1
	ENST00000544925.1	n.56+14946G>A		intron_variant, non_coding_transcript_variant		5
ZBTB16	ENST00000683006.1	n.4702C>T		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21284 AN: 152032 Hom.: 1836 Cov.: 32

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.140 AC: 21287 AN: 152150 Hom.: 1836 Cov.: 32 AF XY: 0.143 AC XY: 10620 AN XY: 74380

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.154

Alfa AF: 0.170 Hom.: 3054

Bravo AF: 0.136

Asia WGS AF: 0.0960 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs566775; hg19: chr11-114125260;