Variant 9-98011296-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_006401.3(ANP32B):c.543C>T(p.Asp181Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000333 in 1,547,996 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0014 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00022 ( 2 hom. )

Consequence

ANP32B
NM_006401.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.801

Variant links:

Genes affected

ANP32B (HGNC:16677): (acidic nuclear phosphoprotein 32 family member B) Enables RNA polymerase binding activity and histone binding activity. Involved in several processes, including activation of cysteine-type endopeptidase activity involved in apoptotic process; nucleosome assembly; and positive regulation of protein export from nucleus. Located in cytoplasm and nucleoplasm. Colocalizes with nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ANP32B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 9-98011296-C-T is Benign according to our data. Variant chr9-98011296-C-T is described in ClinVar as [Benign]. Clinvar id is 746323.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.801 with no splicing effect.

BS2

High AC in GnomAd4 at 206 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANP32B	NM_006401.3 linkuse as main transcript	c.543C>T	p.Asp181Asp	synonymous_variant	5/7	ENST00000339399.5	NP_006392.1	Q92688-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANP32B	ENST00000339399.5 linkuse as main transcript	c.543C>T	p.Asp181Asp	synonymous_variant	5/7	1	NM_006401.3	ENSP00000345848.4		Q92688-1

Frequencies

GnomAD3 genomes

AF:

0.00136

AC:

207

AN:

151916

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00460

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000197

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000735

Gnomad OTH

AF:

0.000959

GnomAD3 exomes

AF:

0.000538

AC:

AN:

159734

Hom.:

AF XY:

0.000407

AC XY:

AN XY:

83552

show subpopulations

Gnomad AFR exome

AF:

0.00518

Gnomad AMR exome

AF:

0.000361

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000782

Gnomad SAS exome

AF:

0.000350

Gnomad FIN exome

AF:

0.0000584

Gnomad NFE exome

AF:

0.000148

Gnomad OTH exome

AF:

0.000436

GnomAD4 exome

AF:

0.000221

AC:

309

AN:

1395962

Hom.:

Cov.:

AF XY:

0.000181

AC XY:

125

AN XY:

688818

show subpopulations

Gnomad4 AFR exome

AF:

0.00450

Gnomad4 AMR exome

AF:

0.000308

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000363

Gnomad4 SAS exome

AF:

0.000227

Gnomad4 FIN exome

AF:

0.0000202

Gnomad4 NFE exome

AF:

0.0000623

Gnomad4 OTH exome

AF:

0.000793

GnomAD4 genome

AF:

0.00135

AC:

206

AN:

152034

Hom.:

Cov.:

AF XY:

0.00136

AC XY:

101

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.00456

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000966

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000736

Gnomad4 OTH

AF:

0.000949

Alfa

AF:

0.000635

Hom.:

Bravo

AF:

0.00155

Asia WGS

AF:

0.00577

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 04, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

7.5

DANN

Benign

0.43

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

3.8

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over