rs7412307

Variant names:

• chr1-43968192-C-G
• rs7412307
• NM_014652.4:c.*510C>G

Variant summary

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

The NM_014652.4(IPO13):​c.*510C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,868 control chromosomes in the GnomAD database, including 35,079 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 0.62 (35079 hom., cov: 30)
• Consequence: IPO13 NM_014652.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 10 publications found

Genes affected

IPO13 (HGNC:16853): (importin 13) This gene encodes a member of the importin-beta family of nuclear transport proteins. The encoded protein mediates the import of specific cargo proteins from the cytoplasm to the nucleus and is dependent on the Ras-related nuclear protein-GTPase system. The encoded protein is also involved in nuclear export of the eukaryotic translation initiation factor 1A.[provided by RefSeq, Mar 2009]

ENSG00000285649 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IPO13	NM_014652.4	c.*510C>G		downstream_gene_variant		ENST00000372343.8	NP_055467.3
IPO13	XM_024451069.2	c.*510C>G		downstream_gene_variant			XP_024306837.1
IPO13	XM_024451070.2	c.*510C>G		downstream_gene_variant			XP_024306838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IPO13	ENST00000372343.8	c.*510C>G		downstream_gene_variant		1	NM_014652.4	ENSP00000361418.3
ENSG00000285649	ENST00000647729.2	n.*159G>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94788 AN: 151750 Hom.: 35075 Cov.: 30

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.624 AC: 94810 AN: 151868 Hom.: 35079 Cov.: 30 AF XY: 0.624 AC XY: 46327 AN XY: 74204

African (AFR) AF: 0.205 AC: 8482 AN: 41364

American (AMR) AF: 0.661 AC: 10087 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2445 AN: 3468

East Asian (EAS) AF: 0.740 AC: 3803 AN: 5142

South Asian (SAS) AF: 0.671 AC: 3216 AN: 4794

European-Finnish (FIN) AF: 0.799 AC: 8435 AN: 10562

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55914 AN: 67960

Other (OTH) AF: 0.677 AC: 1430 AN: 2112

Alfa AF: 0.708 Hom.: 5262

Bravo AF: 0.597

Asia WGS AF: 0.696 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.46
PhyloP100		-0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7412307; hg19: chr1-44433864;