rs1551342

Positions:

• chr15-68793737-G-C

Variant summary

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

The NM_006305.4(ANP32A):​c.55-5818C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,156 control chromosomes in the GnomAD database, including 15,809 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 0.34 (15809 hom., cov: 32)
• Consequence: ANP32A NM_006305.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANP32A	NM_006305.4	c.55-5818C>G		intron_variant		ENST00000465139.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANP32A	ENST00000465139.6	c.55-5818C>G		intron_variant		1	NM_006305.4	P2

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51839 AN: 152038 Hom.: 15749 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.342 AC: 51969 AN: 152156 Hom.: 15809 Cov.: 32 AF XY: 0.344 AC XY: 25592 AN XY: 74394

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.308

Alfa AF: 0.224 Hom.: 1107

Bravo AF: 0.376

Asia WGS AF: 0.501 AC: 1739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.34

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: rs1551342; hg19: chr15-69086076;