rs3739836

Variant names:

• chr9-122921236-G-A
• rs3739836
• NM_020924.4:c.-10-1292C>T

Variant summary

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

The NM_020924.4(ZBTB26):​c.-10-1292C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.083 in 152,144 control chromosomes in the GnomAD database, including 1,661 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 0.083 (1661 hom., cov: 32)
• Consequence: ZBTB26 NM_020924.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

Genes affected

ZBTB26 (HGNC:23383): (zinc finger and BTB domain containing 26) Enables identical protein binding activity and sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB26	NM_020924.4	c.-10-1292C>T		intron_variant	Intron 1 of 1	ENST00000373656.4	NP_065975.1
ZBTB26	NM_001304363.2	c.-10-1292C>T		intron_variant	Intron 1 of 1		NP_001291292.1
ZBTB26	NM_001304364.2	c.-10-1292C>T		intron_variant	Intron 1 of 1		NP_001291293.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB26	ENST00000373656.4	c.-10-1292C>T		intron_variant	Intron 1 of 1	1	NM_020924.4	ENSP00000362760.3
ZBTB26	ENST00000373654.1	c.-10-1292C>T		intron_variant	Intron 1 of 1	2		ENSP00000362758.1

Frequencies

GnomAD3 genomes AF: 0.0828 AC: 12591 AN: 152026 Hom.: 1647 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0675

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0830 AC: 12627 AN: 152144 Hom.: 1661 Cov.: 32 AF XY: 0.0907 AC XY: 6745 AN XY: 74378

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0675

Gnomad4 NFE AF: 0.0426

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0562 Hom.: 223

Bravo AF: 0.0995

Asia WGS AF: 0.344 AC: 1191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.67
DANN	Benign	0.28

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: rs3739836; hg19: chr9-125683515;