2-89913792-A-G

Variant names:

• chr2-89913792-A-G
• rs385951

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.022 (25 hom., cov: 19)
• Consequence: IGK intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.673
• Publications: 0 publications found

Genes affected

IGK (HGNC:5715):

IGKV1D-33 (HGNC:5753): (immunoglobulin kappa variable 1D-33) Enables identical protein binding activity. Predicted to be involved in immune response. Located in blood microparticle and extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS2: High Homozygotes in GnomAd4 at 25 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000390265.2. 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
	IGKV1D-33	ENST00000390265.2	TSL:6	c.-279A>G		upstream_gene	N/A	ENSP00000374800.2	P01593

Frequencies

GnomAD3 genomes AF: 0.0217 AC: 2116 AN: 97460 Hom.: 26 Cov.: 19

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.00378

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.0103

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.00798

Gnomad MID AF: 0.00427

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0270

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

GnomAD4 genome AF: 0.0217 AC: 2116 AN: 97498 Hom.: 25 Cov.: 19 AF XY: 0.0224 AC XY: 1063 AN XY: 47456

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0496 AC: 764 AN: 15410

American (AMR) AF: 0.0230 AC: 228 AN: 9934

Ashkenazi Jewish (ASJ) AF: 0.0103 AC: 29 AN: 2818

East Asian (EAS) AF: 0.0439 AC: 100 AN: 2278

South Asian (SAS) AF: 0.0240 AC: 73 AN: 3042

European-Finnish (FIN) AF: 0.00798 AC: 67 AN: 8398

Middle Eastern (MID) AF: 0.00450 AC: 1 AN: 222

European-Non Finnish (NFE) AF: 0.0153 AC: 812 AN: 53180

Other (OTH) AF: 0.0274 AC: 39 AN: 1422

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00907 Hom.: 16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs385951; hg19: chr2-89952602;