rs3824535

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-122921577-T-A
• chr9-122921577-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_020924.4(ZBTB26):​c.-10-1633A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ZBTB26 NM_020924.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.39
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.7
DANN	Benign	0.72
PhyloP100		2.4

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;