2-23726083-G-T

Variant names:

• chr2-23726083-G-T
• rs7608623
• XM_047444799.1:c.*36+5296C>A

Variant summary

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

The XM_047444799.1(ATAD2B):​c.*36+5296C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,028 control chromosomes in the GnomAD database, including 26,393 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 0.58 (26393 hom., cov: 33)
• Consequence: ATAD2B XM_047444799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 12 publications found

Genes affected

ATAD2B (HGNC:29230): (ATPase family AAA domain containing 2B) The protein encoded by this gene belongs to the AAA ATPase family. This family member includes an N-terminal bromodomain. It has been found to be localized to the nucleus, partly to replication sites, consistent with a chromatin-related function. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATAD2B	XM_047444799.1	c.*36+5296C>A		intron_variant	Intron 30 of 30		XP_047300755.1
ATAD2B	XM_006712030.5	c.4377+28096C>A		intron_variant	Intron 28 of 28		XP_006712093.1
ATAD2B	XR_001738780.3	n.4730+28096C>A		intron_variant	Intron 28 of 30

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88263 AN: 151910 Hom.: 26374 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.581 AC: 88317 AN: 152028 Hom.: 26393 Cov.: 33 AF XY: 0.586 AC XY: 43565 AN XY: 74332

African (AFR) AF: 0.446 AC: 18487 AN: 41414

American (AMR) AF: 0.706 AC: 10796 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3472

East Asian (EAS) AF: 0.786 AC: 4078 AN: 5186

South Asian (SAS) AF: 0.678 AC: 3269 AN: 4822

European-Finnish (FIN) AF: 0.563 AC: 5940 AN: 10556

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41371 AN: 67974

Other (OTH) AF: 0.630 AC: 1331 AN: 2112

Alfa AF: 0.602 Hom.: 74573

Bravo AF: 0.587

Asia WGS AF: 0.714 AC: 2478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.16
PhyloP100		-1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7608623; hg19: chr2-23948953;