rs3739836

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020924.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB26	NM_020924.4	MANE Select	c.-10-1292C>T		intron	N/A	NP_065975.1	Q9HCK0
	ZBTB26	NM_001304363.2		c.-10-1292C>T		intron	N/A	NP_001291292.1	Q9HCK0
	ZBTB26	NM_001304364.2		c.-10-1292C>T		intron	N/A	NP_001291293.1	Q9HCK0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB26	ENST00000373656.4	TSL:1 MANE Select	c.-10-1292C>T		intron	N/A	ENSP00000362760.3	Q9HCK0
	ZBTB26	ENST00000373654.1	TSL:2	c.-10-1292C>T		intron	N/A	ENSP00000362758.1	Q9HCK0
	ZBTB26	ENST00000859132.1		c.-10-1292C>T		intron	N/A	ENSP00000529191.1

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

African (AFR) AF: 0.0324 AC: 1346 AN: 41500

American (AMR) AF: 0.230 AC: 3523 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3470

East Asian (EAS) AF: 0.605 AC: 3134 AN: 5176

South Asian (SAS) AF: 0.105 AC: 505 AN: 4814

European-Finnish (FIN) AF: 0.0675 AC: 714 AN: 10578

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0426 AC: 2896 AN: 67988

Other (OTH) AF: 0.111 AC: 234 AN: 2112

Alfa AF: 0.0553 Hom.: 246

Bravo AF: 0.0995

Asia WGS AF: 0.344 AC: 1191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.67
DANN	Benign	0.28
PhyloP100		-0.55
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: rs3739836; hg19: chr9-125683515;