rs1551343

Variant names:

• chr15-68793418-T-C
• rs1551343
• NM_006305.4:c.55-5499A>G

Variant summary

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

The NM_006305.4(ANP32A):​c.55-5499A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,134 control chromosomes in the GnomAD database, including 5,301 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 0.22 (5301 hom., cov: 32)
• Consequence: ANP32A NM_006305.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANP32A	NM_006305.4	c.55-5499A>G		intron_variant	Intron 1 of 6	ENST00000465139.6	NP_006296.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANP32A	ENST00000465139.6	c.55-5499A>G		intron_variant	Intron 1 of 6	1	NM_006305.4	ENSP00000417864.2

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33738 AN: 152016 Hom.: 5276 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.222 AC: 33809 AN: 152134 Hom.: 5301 Cov.: 32 AF XY: 0.223 AC XY: 16572 AN XY: 74398

African (AFR) AF: 0.440 AC: 18230 AN: 41460

American (AMR) AF: 0.242 AC: 3699 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3472

East Asian (EAS) AF: 0.248 AC: 1280 AN: 5168

South Asian (SAS) AF: 0.224 AC: 1080 AN: 4826

European-Finnish (FIN) AF: 0.0722 AC: 765 AN: 10602

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7389 AN: 67994

Other (OTH) AF: 0.217 AC: 458 AN: 2110

Alfa AF: 0.128 Hom.: 1232

Bravo AF: 0.245

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.64
PhyloP100		0.31
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1551343; hg19: chr15-69085757;