rs11632936

Variant names:

• chr15-68812095-C-A
• rs11632936
• NM_006305.4:c.54+8603G>T

Variant summary

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

The NM_006305.4(ANP32A):​c.54+8603G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,812 control chromosomes in the GnomAD database, including 4,989 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 0.23 (4989 hom., cov: 31)
• Consequence: ANP32A NM_006305.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 1 publications found

Genes affected

ANP32A (HGNC:13233): (acidic nuclear phosphoprotein 32 family member A) Enables RNA binding activity. Involved in nucleocytoplasmic transport. Located in endoplasmic reticulum; nucleus; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006305.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANP32A	NM_006305.4	MANE Select	c.54+8603G>T		intron	N/A	NP_006296.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANP32A	ENST00000465139.6	TSL:1 MANE Select	c.54+8603G>T		intron	N/A	ENSP00000417864.2
	ANP32A	ENST00000882112.1		c.54+8603G>T		intron	N/A	ENSP00000552171.1
	ANP32A	ENST00000923067.1		c.54+8603G>T		intron	N/A	ENSP00000593126.1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34827 AN: 151696 Hom.: 4997 Cov.: 31

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.229 AC: 34821 AN: 151812 Hom.: 4989 Cov.: 31 AF XY: 0.228 AC XY: 16928 AN XY: 74176

African (AFR) AF: 0.0668 AC: 2768 AN: 41410

American (AMR) AF: 0.215 AC: 3280 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 972 AN: 3468

East Asian (EAS) AF: 0.133 AC: 687 AN: 5158

South Asian (SAS) AF: 0.413 AC: 1984 AN: 4806

European-Finnish (FIN) AF: 0.282 AC: 2961 AN: 10502

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21279 AN: 67908

Other (OTH) AF: 0.241 AC: 508 AN: 2110

Alfa AF: 0.252 Hom.: 9590

Bravo AF: 0.211

Asia WGS AF: 0.250 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.70
PhyloP100		-0.65
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: rs11632936; hg19: chr15-69104434;