rs1551344

Positions:

• chr15-68793207-T-A
• chr15-68793207-T-G

Variant summary

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

The NM_006305.4(ANP32A):​c.55-5288A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,230 control chromosomes in the GnomAD database, including 2,310 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 0.15 (2310 hom., cov: 32)
• Consequence: ANP32A NM_006305.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532

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]

ANP32A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANP32A	NM_006305.4	c.55-5288A>T		intron_variant		ENST00000465139.6	NP_006296.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANP32A	ENST00000465139.6	c.55-5288A>T		intron_variant		1	NM_006305.4	ENSP00000417864.2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22116 AN: 152112 Hom.: 2308 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0674

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.145 AC: 22139 AN: 152230 Hom.: 2310 Cov.: 32 AF XY: 0.148 AC XY: 11043 AN XY: 74432

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.0749

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0280 Hom.: 14

Bravo AF: 0.161

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.92

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: rs1551344; hg19: chr15-69085546;