rs7583495

Variant names:

• chr2-90028788-G-A
• rs7583495

Your query was ambiguous. Multiple possible variants found:

• chr2-90028788-G-A
• chr2-90028788-G-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 0.0828 in 150,738 control chromosomes in the GnomAD database, including 998 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 0.083 (998 hom., cov: 31)
• Consequence: IGK intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 0 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 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: 0.0827 AC: 12458 AN: 150620 Hom.: 993 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0543

Gnomad ASJ AF: 0.0367

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0709

Gnomad FIN AF: 0.0620

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.0528

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

GnomAD4 genome AF: 0.0828 AC: 12482 AN: 150738 Hom.: 998 Cov.: 31 AF XY: 0.0789 AC XY: 5810 AN XY: 73616

African (AFR) AF: 0.139 AC: 5666 AN: 40732

American (AMR) AF: 0.0541 AC: 824 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0367 AC: 127 AN: 3456

East Asian (EAS) AF: 0.0163 AC: 83 AN: 5104

South Asian (SAS) AF: 0.0703 AC: 334 AN: 4748

European-Finnish (FIN) AF: 0.0620 AC: 649 AN: 10464

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0689 AC: 4664 AN: 67726

Other (OTH) AF: 0.0523 AC: 109 AN: 2086

Alfa AF: 0.0780 Hom.: 96

Bravo AF: 0.0838

Asia WGS AF: 0.0430 AC: 148 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.017
DANN	Benign	0.68
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7583495; hg19: chr2-90067598;