rs2924633

Variant names:

• chr15-68802300-T-C
• rs2924633
• NM_006305.4:c.55-14381A>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.55-14381A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,076 control chromosomes in the GnomAD database, including 13,876 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 0.42 (13876 hom., cov: 32)
• Consequence: ANP32A NM_006305.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500
• Publications: 8 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 (SAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006305.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANP32A	NM_006305.4	MANE Select	c.55-14381A>G		intron	N/A	NP_006296.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANP32A	ENST00000465139.6	TSL:1 MANE Select	c.55-14381A>G		intron	N/A	ENSP00000417864.2
	ANP32A	ENST00000882112.1		c.55-14108A>G		intron	N/A	ENSP00000552171.1
	ANP32A	ENST00000923067.1		c.55-14108A>G		intron	N/A	ENSP00000593126.1

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64095 AN: 151958 Hom.: 13855 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.422 AC: 64162 AN: 152076 Hom.: 13876 Cov.: 32 AF XY: 0.419 AC XY: 31172 AN XY: 74346

African (AFR) AF: 0.494 AC: 20475 AN: 41480

American (AMR) AF: 0.349 AC: 5341 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1227 AN: 5176

South Asian (SAS) AF: 0.520 AC: 2506 AN: 4820

European-Finnish (FIN) AF: 0.358 AC: 3781 AN: 10552

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27717 AN: 67976

Other (OTH) AF: 0.443 AC: 933 AN: 2106

Alfa AF: 0.413 Hom.: 18965

Bravo AF: 0.417

Asia WGS AF: 0.370 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.64
PhyloP100		0.050
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: rs2924633; hg19: chr15-69094639;