9-122921577-T-G

Variant names:

• chr9-122921577-T-G
• rs3824535
• NM_020924.4:c.-10-1633A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020924.4(ZBTB26):​c.-10-1633A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,164 control chromosomes in the GnomAD database, including 5,449 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 0.23 (5449 hom., cov: 33)
• Consequence: ZBTB26 NM_020924.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.39
• Publications: 11 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB26	NM_020924.4	c.-10-1633A>C		intron_variant	Intron 1 of 1	ENST00000373656.4	NP_065975.1
ZBTB26	NM_001304363.2	c.-10-1633A>C		intron_variant	Intron 1 of 1		NP_001291292.1
ZBTB26	NM_001304364.2	c.-10-1633A>C		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.-10-1633A>C		intron_variant	Intron 1 of 1	1	NM_020924.4	ENSP00000362760.3
ZBTB26	ENST00000373654.1	c.-10-1633A>C		intron_variant	Intron 1 of 1	2		ENSP00000362758.1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34719 AN: 152046 Hom.: 5411 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.229 AC: 34825 AN: 152164 Hom.: 5449 Cov.: 33 AF XY: 0.234 AC XY: 17403 AN XY: 74392

African (AFR) AF: 0.353 AC: 14633 AN: 41490

American (AMR) AF: 0.312 AC: 4761 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3464

East Asian (EAS) AF: 0.651 AC: 3362 AN: 5166

South Asian (SAS) AF: 0.130 AC: 626 AN: 4828

European-Finnish (FIN) AF: 0.167 AC: 1774 AN: 10604

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8483 AN: 68014

Other (OTH) AF: 0.231 AC: 488 AN: 2110

Alfa AF: 0.147 Hom.: 1084

Bravo AF: 0.253

Asia WGS AF: 0.400 AC: 1388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.8
DANN	Benign	0.72
PhyloP100		2.4
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: rs3824535; hg19: chr9-125683856;