13-22838450-C-G

Variant names:

• chr13-22838450-C-G
• rs9506942

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;