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. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGL		n.22196484T>C		intragenic_variant
IGLV6-57	unassigned_transcript_3567	c.*208T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGLV6-57	ENST00000390285.4	c.*208T>C		downstream_gene_variant		6		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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.152

Alfa AF: 0.172 Hom.: 3298

Bravo AF: 0.178

Asia WGS AF: 0.201 AC: 697 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.71
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2073449; hg19: chr22-22550884;