NM_001243702.2:c.3+260T>G

Variant names:

• chr18-5292984-A-C
• rs9952350
• NM_001243702.2:c.3+260T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZBTB14	NM_001243702.2	c.3+260T>G		intron_variant	Intron 3 of 3	ENST00000651870.1	NP_001230631.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB14	ENST00000651870.1	c.3+260T>G		intron_variant	Intron 3 of 3		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

African (AFR) AF: 0.473 AC: 19619 AN: 41442

American (AMR) AF: 0.365 AC: 5572 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1899 AN: 3468

East Asian (EAS) AF: 0.0744 AC: 385 AN: 5176

South Asian (SAS) AF: 0.450 AC: 2171 AN: 4828

European-Finnish (FIN) AF: 0.393 AC: 4152 AN: 10566

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30109 AN: 67994

Other (OTH) AF: 0.430 AC: 908 AN: 2112

Alfa AF: 0.433 Hom.: 42058

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
PhyloP100		-5.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9952350; hg19: chr18-5292983;