rs7164503

Variant names:

• chr15-68789051-T-C
• rs7164503
• NM_006305.4:c.55-1132A>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.55-1132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,056 control chromosomes in the GnomAD database, including 9,189 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 0.27 (9189 hom., cov: 32)
• Consequence: ANP32A NM_006305.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANP32A	NM_006305.4	c.55-1132A>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.55-1132A>G		intron_variant	Intron 1 of 6	1	NM_006305.4	ENSP00000417864.2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41270 AN: 151934 Hom.: 9161 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.0375

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.272 AC: 41362 AN: 152056 Hom.: 9189 Cov.: 32 AF XY: 0.273 AC XY: 20310 AN XY: 74344

African (AFR) AF: 0.592 AC: 24530 AN: 41450

American (AMR) AF: 0.256 AC: 3912 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2545 AN: 5180

South Asian (SAS) AF: 0.178 AC: 854 AN: 4810

European-Finnish (FIN) AF: 0.132 AC: 1399 AN: 10568

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7034 AN: 67990

Other (OTH) AF: 0.246 AC: 519 AN: 2106

Alfa AF: 0.182 Hom.: 8650

Bravo AF: 0.298

Asia WGS AF: 0.349 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.32
PhyloP100		-0.95
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: rs7164503; hg19: chr15-69081390;