rs2081302

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ATAD2B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ATAD2B	XM_006712030.5	c.4378-31365T>G		intron_variant			XP_006712093.1
ATAD2B	XM_047444799.1	c.*36+8894T>G		intron_variant			XP_047300755.1
ATAD2B	XR_001738780.3	n.4731-31365T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.619

Alfa AF: 0.601 Hom.: 4406

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2081302; hg19: chr2-23945355;