rs7164503

chr15-68789051-T-C

Variant summary

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

The NM_006305.4(ANP32A):c.55-1132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,056 control chromosomes in the GnomAD database, including 9,189 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 0.27 (9189 hom., cov: 32)
• Consequence: ANP32A NM_006305.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANP32A	NM_006305.4	c.55-1132A>G		intron_variant		ENST00000465139.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANP32A	ENST00000465139.6	c.55-1132A>G		intron_variant		1	NM_006305.4	P2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41270 AN: 151934 Hom.: 9161 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.0375

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.272 AC: 41362 AN: 152056 Hom.: 9189 Cov.: 32 AF XY: 0.273 AC XY: 20310 AN XY: 74344

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.246

Alfa AF: 0.134 Hom.: 2791

Bravo AF: 0.298

Asia WGS AF: 0.349 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.37
Dann	Benign	0.32

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: rs7164503; hg19: chr15-69081390;