9-98001608-C-G

Position:

• chr9-98001608-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006401.3(ANP32B):​c.327+2930C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,974 control chromosomes in the GnomAD database, including 5,175 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 0.25 (5175 hom., cov: 31)
• Consequence: ANP32B NM_006401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANP32B	NM_006401.3	c.327+2930C>G		intron_variant		ENST00000339399.5	NP_006392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANP32B	ENST00000339399.5	c.327+2930C>G		intron_variant		1	NM_006401.3	ENSP00000345848.4
ANP32B	ENST00000473205.1	n.375-668C>G		intron_variant		3
ANP32B	ENST00000486769.1	n.65+2930C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37853 AN: 151856 Hom.: 5174 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.251

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.249 AC: 37868 AN: 151974 Hom.: 5175 Cov.: 31 AF XY: 0.251 AC XY: 18620 AN XY: 74264

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.253

Alfa AF: 0.0862 Hom.: 113

Bravo AF: 0.249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.68

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

Other links and lift over

dbSNP: rs7850685; hg19: chr9-100763890;