chr18-5292984-A-C

Position:

• chr18-5292984-A-C

Variant summary

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

The NM_001243702.2(ZBTB14):​c.3+260T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,060 control chromosomes in the GnomAD database, including 14,596 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 0.43 (14596 hom., cov: 33)
• Consequence: ZBTB14 NM_001243702.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.29

Genes affected

ZBTB14 (HGNC:12860): (zinc finger and BTB domain containing 14) Enables DNA-binding transcription factor activity and transcription cis-regulatory region binding activity. Involved in negative regulation of transcription, DNA-templated. Located in aggresome; cytosol; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB14	NM_001243702.2	c.3+260T>G		intron_variant		ENST00000651870.1	NP_001230631.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB14	ENST00000651870.1	c.3+260T>G		intron_variant			NM_001243702.2	ENSP00000499212.1

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65272 AN: 151942 Hom.: 14583 Cov.: 33

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.0744

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.430 AC: 65319 AN: 152060 Hom.: 14596 Cov.: 33 AF XY: 0.425 AC XY: 31564 AN XY: 74342

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.0744

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.430

Alfa AF: 0.434 Hom.: 22844

Bravo AF: 0.427

Asia WGS AF: 0.312 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.37
DANN	Benign	0.19

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: rs9952350; hg19: chr18-5292983;