2-23722485-A-C

Variant names:

• chr2-23722485-A-C
• rs2081302
• XM_047444799.1:c.*36+8894T>G

Variant summary

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

The XR_001738780.3(ATAD2B):​n.4731-31365T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,018 control chromosomes in the GnomAD database, including 25,697 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 0.57 (25697 hom., cov: 32)
• Consequence: ATAD2B XR_001738780.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 7 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=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 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: 0.574 AC: 87216 AN: 151900 Hom.: 25689 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.574 AC: 87244 AN: 152018 Hom.: 25697 Cov.: 32 AF XY: 0.580 AC XY: 43081 AN XY: 74316

African (AFR) AF: 0.448 AC: 18548 AN: 41446

American (AMR) AF: 0.696 AC: 10636 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2179 AN: 3472

East Asian (EAS) AF: 0.794 AC: 4109 AN: 5172

South Asian (SAS) AF: 0.677 AC: 3267 AN: 4828

European-Finnish (FIN) AF: 0.566 AC: 5960 AN: 10534

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40401 AN: 67958

Other (OTH) AF: 0.619 AC: 1307 AN: 2112

Alfa AF: 0.597 Hom.: 4488

Bravo AF: 0.579

Asia WGS AF: 0.709 AC: 2457 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.8
DANN	Benign	0.89
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2081302; hg19: chr2-23945355;