chr10-80130-C-T

Variant names:

• chr10-80130-C-T
• rs11591988

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 0.122 in 152,156 control chromosomes in the GnomAD database, including 2,047 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 0.12 (2047 hom., cov: 32)
• Consequence: IL9RP2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 6 publications found

Genes affected

IL9RP2 (HGNC:6032): (IL9R pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18541 AN: 152038 Hom.: 2037 Cov.: 32

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.122 AC: 18549 AN: 152156 Hom.: 2047 Cov.: 32 AF XY: 0.130 AC XY: 9695 AN XY: 74370

African (AFR) AF: 0.0262 AC: 1090 AN: 41546

American (AMR) AF: 0.229 AC: 3492 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3470

East Asian (EAS) AF: 0.529 AC: 2723 AN: 5144

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4812

European-Finnish (FIN) AF: 0.165 AC: 1752 AN: 10602

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7511 AN: 67994

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.116 Hom.: 2342

Bravo AF: 0.126

Asia WGS AF: 0.342 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.55
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs11591988; hg19: chr10-126070;