rs9506942

Variant names:

• chr13-22838450-C-G
• rs9506942

Your query was ambiguous. Multiple possible variants found:

• chr13-22838450-C-G
• chr13-22838450-C-T

Variant summary

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

The variant allele was found at a frequency of 0.368 in 152,026 control chromosomes in the GnomAD database, including 11,653 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 0.37 (11653 hom., cov: 33)
• Consequence: IPMKP1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23
• Publications: 5 publications found

Genes affected

IPMKP1 (HGNC:39354): (inositol polyphosphate multikinase pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IPMKP1		n.22838450C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56000 AN: 151910 Hom.: 11653 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.368 AC: 56009 AN: 152026 Hom.: 11653 Cov.: 33 AF XY: 0.372 AC XY: 27651 AN XY: 74322

African (AFR) AF: 0.181 AC: 7504 AN: 41500

American (AMR) AF: 0.311 AC: 4759 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1203 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2764 AN: 5102

South Asian (SAS) AF: 0.427 AC: 2059 AN: 4820

European-Finnish (FIN) AF: 0.529 AC: 5601 AN: 10596

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30869 AN: 67920

Other (OTH) AF: 0.377 AC: 796 AN: 2114

Alfa AF: 0.301 Hom.: 882

Bravo AF: 0.341

Asia WGS AF: 0.426 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.9
DANN	Benign	0.12
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs9506942; hg19: chr13-23412589;