rs7850685

chr9-98001608-C-Achr9-98001608-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_006401.3(ANP32B):c.327+2930C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00155 in 152,032 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0016 (0 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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS2: High AC in GnomAd at 236 AD gene.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANP32B	ENST00000339399.5	c.327+2930C>A		intron_variant		1	NM_006401.3	P1
ANP32B	ENST00000473205.1	n.375-668C>A		intron_variant, non_coding_transcript_variant		3
ANP32B	ENST00000486769.1	n.65+2930C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00155 AC: 236 AN: 151914 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000532

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00125

Gnomad FIN AF: 0.000380

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00282

Gnomad OTH AF: 0.000958

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

GnomAD4 genome AF: 0.00155 AC: 236 AN: 152032 Hom.: 0 Cov.: 31 AF XY: 0.00155 AC XY: 115 AN XY: 74294

Gnomad4 AFR AF: 0.000530

Gnomad4 AMR AF: 0.000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00125

Gnomad4 FIN AF: 0.000380

Gnomad4 NFE AF: 0.00282

Gnomad4 OTH AF: 0.000948

Alfa AF: 0.000294 Hom.: 113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.1
Dann	Benign	0.74

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;