rs842164

Variant names:

• chr2-90198576-G-T
• rs842164

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 0.65 in 150,096 control chromosomes in the GnomAD database, including 35,190 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 0.65 (35190 hom., cov: 31)
• Consequence: IGK intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 4 publications found

Genes affected

IGK (HGNC:5715):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.650 AC: 97518 AN: 149986 Hom.: 35168 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.650 AC: 97563 AN: 150096 Hom.: 35190 Cov.: 31 AF XY: 0.660 AC XY: 48340 AN XY: 73188

African (AFR) AF: 0.369 AC: 14962 AN: 40580

American (AMR) AF: 0.769 AC: 11617 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2337 AN: 3464

East Asian (EAS) AF: 0.870 AC: 4427 AN: 5086

South Asian (SAS) AF: 0.782 AC: 3677 AN: 4702

European-Finnish (FIN) AF: 0.818 AC: 8458 AN: 10336

Middle Eastern (MID) AF: 0.563 AC: 161 AN: 286

European-Non Finnish (NFE) AF: 0.736 AC: 49687 AN: 67542

Other (OTH) AF: 0.701 AC: 1456 AN: 2076

Alfa AF: 0.708 Hom.: 38444

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs842164; hg19: chr2-90237441;