Variant chr2-23900669-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017552.4(ATAD2B):c.217-4699G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,022 control chromosomes in the GnomAD database, including 13,693 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 0.41 ( 13691 hom., cov: 31)

Exomes 𝑓: 0.36 ( 2 hom. )

Consequence

ATAD2B
NM_017552.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.50

Variant links:

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]

ATAD2B links:

RPS13P4 (HGNC:35731): (ribosomal protein S13 pseudogene 4)

RPS13P4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATAD2B	NM_017552.4 linkuse as main transcript	c.217-4699G>A		intron_variant		ENST00000238789.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
ATAD2B	ENST00000238789.10 linkuse as main transcript	c.217-4699G>A	intron_variant	5	NM_017552.4	P1
ATAD2B	ENST00000439915.1 linkuse as main transcript	c.217-4699G>A	intron_variant	1
RPS13P4	ENST00000421721.1 linkuse as main transcript		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.407

AC:

61771

AN:

151882

Hom.:

13675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.269

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.569

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.770

Gnomad SAS

AF:

0.465

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.439

GnomAD4 exome

AF:

0.364

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.333

GnomAD4 genome

AF:

0.407

AC:

61806

AN:

152000

Hom.:

13691

Cov.:

AF XY:

0.414

AC XY:

30777

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.269

Gnomad4 AMR

AF:

0.569

Gnomad4 ASJ

AF:

0.449

Gnomad4 EAS

AF:

0.770

Gnomad4 SAS

AF:

0.466

Gnomad4 FIN

AF:

0.421

Gnomad4 NFE

AF:

0.415

Gnomad4 OTH

AF:

0.444

Alfa

AF:

0.435

Hom.:

2709

Bravo

AF:

0.415

Asia WGS

AF:

0.603

AC:

2093

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.5

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over