rs2081302

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-23722485-A-C
• chr2-23722485-A-T

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+8894T>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 XM_047444799.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATAD2B	XM_047444799.1	c.*36+8894T>G		intron_variant	Intron 30 of 30		XP_047300755.1
ATAD2B	XM_006712030.5	c.4378-31365T>G		intron_variant	Intron 28 of 28		XP_006712093.1
ATAD2B	XR_001738780.3	n.4731-31365T>G		intron_variant	Intron 28 of 30

Ensembl

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

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 v4.3

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;