rs11632936

Positions:

• chr15-68812095-C-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANP32A	NM_006305.4	c.54+8603G>T		intron_variant		ENST00000465139.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANP32A	ENST00000465139.6	c.54+8603G>T		intron_variant		1	NM_006305.4	P2

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

Gnomad4 AFR AF: 0.0668

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.241

Alfa AF: 0.272 Hom.: 6314

Bravo AF: 0.211

Asia WGS AF: 0.250 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.70

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: rs11632936; hg19: chr15-69104434;