1-43948455-C-G

Variant summary

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

The NM_014652.4(IPO13):c.84+771C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,306 control chromosomes in the GnomAD database, including 4,161 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 0.21 (4161 hom., cov: 34)
• Consequence: IPO13 NM_014652.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IPO13	NM_014652.4	c.84+771C>G		intron_variant		ENST00000372343.8
IPO13	XM_024451069.2	c.-83+771C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IPO13	ENST00000372343.8	c.84+771C>G		intron_variant		1	NM_014652.4	P1
IPO13	ENST00000489061.1	n.130+771C>G		intron_variant, non_coding_transcript_variant		3
IPO13	ENST00000489773.5	n.115+771C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32441 AN: 152188 Hom.: 4164 Cov.: 34

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.213 AC: 32476 AN: 152306 Hom.: 4161 Cov.: 34 AF XY: 0.214 AC XY: 15936 AN XY: 74468

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.0920

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.202

Alfa AF: 0.0816 Hom.: 127

Bravo AF: 0.227

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	7.8
Dann	Benign	0.36

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: rs1990150; hg19: chr1-44414127;