9-97983620-A-G

Position:

• chr9-97983620-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_006401.3(ANP32B):​c.54+11A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,557,716 control chromosomes in the GnomAD database, including 47,869 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.26 (5614 hom., cov: 33)
  • Exomes 𝑓: 0.23 (42255 hom.)
• Consequence: ANP32B NM_006401.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.409

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]

LOC124902226 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 9-97983620-A-G is Benign according to our data. Variant chr9-97983620-A-G is described in ClinVar as [Benign]. Clinvar id is 1230639.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANP32B	NM_006401.3	c.54+11A>G		intron_variant		ENST00000339399.5	NP_006392.1
LOC124902226	XR_007061686.1	n.454+3026T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANP32B	ENST00000339399.5	c.54+11A>G		intron_variant		1	NM_006401.3	ENSP00000345848.4

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39041 AN: 151846 Hom.: 5608 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.258

GnomAD3 exomes AF: 0.249 AC: 43057 AN: 173144 Hom.: 6469 AF XY: 0.261 AC XY: 24335 AN XY: 93186

Gnomad AFR exome AF: 0.351

Gnomad AMR exome AF: 0.215

Gnomad ASJ exome AF: 0.233

Gnomad EAS exome AF: 0.101

Gnomad SAS exome AF: 0.499

Gnomad FIN exome AF: 0.206

Gnomad NFE exome AF: 0.207

Gnomad OTH exome AF: 0.240

GnomAD4 exome AF: 0.233 AC: 327267 AN: 1405764 Hom.: 42255 Cov.: 30 AF XY: 0.240 AC XY: 166908 AN XY: 695888

Gnomad4 AFR exome AF: 0.366

Gnomad4 AMR exome AF: 0.217

Gnomad4 ASJ exome AF: 0.228

Gnomad4 EAS exome AF: 0.0854

Gnomad4 SAS exome AF: 0.488

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.216

Gnomad4 OTH exome AF: 0.244

GnomAD4 genome AF: 0.257 AC: 39068 AN: 151952 Hom.: 5614 Cov.: 33 AF XY: 0.259 AC XY: 19202 AN XY: 74272

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.259

Alfa AF: 0.199 Hom.: 1107

Bravo AF: 0.257

Asia WGS AF: 0.329 AC: 1142 AN: 3472

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 15, 2020	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.6
DANN	Benign	0.34
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3739672; hg19: chr9-100745902; COSMIC: COSV59587704; COSMIC: COSV59587704;