rs1551342

Variant names:

• chr15-68793737-G-C
• rs1551342
• NM_006305.4:c.55-5818C>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.55-5818C>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
• Publications: 1 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=-0.91).
• 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 rank	MANE	Protein	UniProt
ANP32A	NM_006305.4	c.55-5818C>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.55-5818C>G		intron_variant	Intron 1 of 6	1	NM_006305.4	ENSP00000417864.2

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

African (AFR) AF: 0.786 AC: 32613 AN: 41496

American (AMR) AF: 0.298 AC: 4549 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3472

East Asian (EAS) AF: 0.718 AC: 3714 AN: 5172

South Asian (SAS) AF: 0.239 AC: 1153 AN: 4822

European-Finnish (FIN) AF: 0.159 AC: 1685 AN: 10596

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7003 AN: 68002

Other (OTH) AF: 0.308 AC: 650 AN: 2110

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
PhyloP100		-2.0
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: rs1551342; hg19: chr15-69086076;