chr2-23726083-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 XR_001738780.3(ATAD2B):​n.4730+28096C>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 XR_001738780.3 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;