2-90203210-A-T

Variant names:

• chr2-90203210-A-T
• rs842160

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0254 in 150,922 control chromosomes in the GnomAD database, including 200 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 0.025 (200 hom., cov: 32)
• Consequence: IGK intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 3 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=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0254 (3834/150922) while in subpopulation NFE AF = 0.0346 (2345/67754). AF 95% confidence interval is 0.0334. There are 200 homozygotes in GnomAd4. There are 1764 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 200 gene

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: 0.0255 AC: 3838 AN: 150804 Hom.: 200 Cov.: 32

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0626

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0196

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0254 AC: 3834 AN: 150922 Hom.: 200 Cov.: 32 AF XY: 0.0239 AC XY: 1764 AN XY: 73698

African (AFR) AF: 0.0136 AC: 555 AN: 40822

American (AMR) AF: 0.0243 AC: 370 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.0626 AC: 217 AN: 3468

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5140

South Asian (SAS) AF: 0.0196 AC: 93 AN: 4752

European-Finnish (FIN) AF: 0.0133 AC: 140 AN: 10500

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0346 AC: 2345 AN: 67754

Other (OTH) AF: 0.0303 AC: 63 AN: 2080

Alfa AF: 0.0111 Hom.: 10

Bravo AF: 0.0257

Asia WGS AF: 0.00405 AC: 14 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.54
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs842160; hg19: chr2-90242076;