2-90038664-A-G

Variant names:

• chr2-90038664-A-G
• rs2847840

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 0.906 in 150,372 control chromosomes in the GnomAD database, including 62,241 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 0.91 (62241 hom., cov: 31)
• Consequence: IGK intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 5 publications found

Genes affected

IGK (HGNC:5715):

IGKV3D-20 (HGNC:5825): (immunoglobulin kappa variable 3D-20) Predicted to be involved in immune response. Predicted to be located in extracellular region and plasma membrane. Predicted to be part of immunoglobulin complex. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGK		n.90038664A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGKV3D-20	ENST00000390270.2	c.-281A>G		upstream_gene_variant		6		ENSP00000374805.2

Frequencies

GnomAD3 genomes AF: 0.906 AC: 136124 AN: 150252 Hom.: 62171 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.906 AC: 136256 AN: 150372 Hom.: 62241 Cov.: 31 AF XY: 0.908 AC XY: 66684 AN XY: 73406

African (AFR) AF: 0.940 AC: 38164 AN: 40600

American (AMR) AF: 0.918 AC: 13937 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2924 AN: 3462

East Asian (EAS) AF: 0.934 AC: 4749 AN: 5084

South Asian (SAS) AF: 0.912 AC: 4320 AN: 4736

European-Finnish (FIN) AF: 0.921 AC: 9577 AN: 10402

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 59697 AN: 67632

Other (OTH) AF: 0.885 AC: 1831 AN: 2068

Alfa AF: 0.908 Hom.: 36456

Bravo AF: 0.908

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.68
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2847840; hg19: chr2-90077496;