rs2073449

Variant names:

• chr22-22196484-T-C
• rs2073449

Your query was ambiguous. Multiple possible variants found:

• chr22-22196484-T-C
• chr22-22196484-T-G

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 0.179 in 152,098 control chromosomes in the GnomAD database, including 2,755 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 0.18 (2755 hom., cov: 32)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 5 publications found

Genes affected

IGL (HGNC:5853):

IGLV6-57 (HGNC:5927): (immunoglobulin lambda variable 6-57) 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000390285.4. You can select a different transcript below to see updated ACMG assignments.

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
	IGLV6-57	ENST00000390285.4	TSL:6	c.*208T>C		downstream_gene	N/A	ENSP00000374820.4

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27186 AN: 151984 Hom.: 2755 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.179 AC: 27206 AN: 152098 Hom.: 2755 Cov.: 32 AF XY: 0.186 AC XY: 13839 AN XY: 74364

African (AFR) AF: 0.113 AC: 4678 AN: 41526

American (AMR) AF: 0.262 AC: 4004 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3464

East Asian (EAS) AF: 0.259 AC: 1328 AN: 5134

South Asian (SAS) AF: 0.204 AC: 983 AN: 4808

European-Finnish (FIN) AF: 0.274 AC: 2901 AN: 10574

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.182 AC: 12376 AN: 67988

Other (OTH) AF: 0.152 AC: 321 AN: 2116

Alfa AF: 0.174 Hom.: 4268

Bravo AF: 0.178

Asia WGS AF: 0.201 AC: 697 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.71
DANN	Benign	0.34
PhyloP100		-2.5
Mutation Taster		=93/7	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2073449; hg19: chr22-22550884;