rs1551345

Variant names:

• chr15-68793194-T-C
• rs1551345
• NM_006305.4:c.55-5275A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_006305.4(ANP32A):​c.55-5275A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,214 control chromosomes in the GnomAD database, including 2,829 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 0.16 (2829 hom., cov: 32)
• Consequence: ANP32A NM_006305.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530
• Publications: 2 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANP32A	NM_006305.4	c.55-5275A>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.55-5275A>G		intron_variant	Intron 1 of 6	1	NM_006305.4	ENSP00000417864.2

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24735 AN: 152096 Hom.: 2827 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0902

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.163 AC: 24759 AN: 152214 Hom.: 2829 Cov.: 32 AF XY: 0.165 AC XY: 12283 AN XY: 74428

African (AFR) AF: 0.298 AC: 12386 AN: 41504

American (AMR) AF: 0.202 AC: 3082 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0902 AC: 313 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1878 AN: 5172

South Asian (SAS) AF: 0.0867 AC: 419 AN: 4830

European-Finnish (FIN) AF: 0.111 AC: 1183 AN: 10616

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0752 AC: 5116 AN: 68012

Other (OTH) AF: 0.149 AC: 315 AN: 2112

Alfa AF: 0.108 Hom.: 1085

Bravo AF: 0.180

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	16
DANN	Benign	0.80
PhyloP100		0.53
Mutation Taster		=99/1	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: rs1551345; hg19: chr15-69085533;