2-23900669-C-T

Variant names:

• chr2-23900669-C-T
• rs17711796
• NM_017552.4:c.217-4699G>A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 5 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]

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ATAD2B	NM_017552.4	c.217-4699G>A		intron_variant	Intron 1 of 27	ENST00000238789.10	NP_060022.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATAD2B	ENST00000238789.10	c.217-4699G>A		intron_variant	Intron 1 of 27	5	NM_017552.4	ENSP00000238789.5
ATAD2B	ENST00000439915.1	c.217-4699G>A		intron_variant	Intron 1 of 9	1		ENSP00000403177.1
RPS13P4	ENST00000421721.1	n.-24C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61771 AN: 151882 Hom.: 13675 Cov.: 31

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: 8 AN: 22 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 8 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 6 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.407 AC: 61806 AN: 152000 Hom.: 13691 Cov.: 31 AF XY: 0.414 AC XY: 30777 AN XY: 74260

African (AFR) AF: 0.269 AC: 11142 AN: 41464

American (AMR) AF: 0.569 AC: 8688 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1556 AN: 3466

East Asian (EAS) AF: 0.770 AC: 3982 AN: 5174

South Asian (SAS) AF: 0.466 AC: 2246 AN: 4822

European-Finnish (FIN) AF: 0.421 AC: 4431 AN: 10536

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28226 AN: 67968

Other (OTH) AF: 0.444 AC: 936 AN: 2108

Alfa AF: 0.382 Hom.: 3383

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
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17711796; hg19: chr2-24123539;