rs2958405

Variant names:

• chr15-68805267-G-A
• rs2958405
• NM_006305.4:c.54+15431C>T

Variant summary

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

The NM_006305.4(ANP32A):​c.54+15431C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,118 control chromosomes in the GnomAD database, including 13,827 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 0.41 (13827 hom., cov: 33)
• Consequence: ANP32A NM_006305.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 7 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]

ANP32A-IT1 (HGNC:25672): (ANP32A intronic transcript 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANP32A	NM_006305.4	c.54+15431C>T		intron_variant	Intron 1 of 6	ENST00000465139.6	NP_006296.1
ANP32A-IT1	NR_026808.1	n.1835C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANP32A	ENST00000465139.6	c.54+15431C>T		intron_variant	Intron 1 of 6	1	NM_006305.4	ENSP00000417864.2

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62429 AN: 152000 Hom.: 13809 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.411 AC: 62494 AN: 152118 Hom.: 13827 Cov.: 33 AF XY: 0.420 AC XY: 31237 AN XY: 74356

African (AFR) AF: 0.479 AC: 19859 AN: 41494

American (AMR) AF: 0.484 AC: 7390 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 921 AN: 3466

East Asian (EAS) AF: 0.796 AC: 4118 AN: 5172

South Asian (SAS) AF: 0.496 AC: 2394 AN: 4824

European-Finnish (FIN) AF: 0.400 AC: 4231 AN: 10570

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22398 AN: 67992

Other (OTH) AF: 0.400 AC: 845 AN: 2112

Alfa AF: 0.366 Hom.: 21280

Bravo AF: 0.423

Asia WGS AF: 0.621 AC: 2157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.52
PhyloP100		-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: rs2958405; hg19: chr15-69097606; COSMIC: COSV51189897; COSMIC: COSV51189897;