chr2-89228414-A-G

Variant names:

• chr2-89228414-A-G
• rs375385

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.079 (871 hom., cov: 26)
  • Failed GnomAD Quality Control
• Consequence: IGK intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 2 publications found

Genes affected

IGK (HGNC:5715):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.12).

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: 0.0794 AC: 8460 AN: 106500 Hom.: 867 Cov.: 26

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0130

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.0503

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.0218

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.0407

Gnomad OTH AF: 0.0727

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0794 AC: 8463 AN: 106534 Hom.: 871 Cov.: 26 AF XY: 0.0724 AC XY: 3770 AN XY: 52100

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

African (AFR) AF: 0.211 AC: 3895 AN: 18440

American (AMR) AF: 0.0925 AC: 973 AN: 10514

Ashkenazi Jewish (ASJ) AF: 0.0503 AC: 139 AN: 2764

East Asian (EAS) AF: 0.192 AC: 493 AN: 2564

South Asian (SAS) AF: 0.0896 AC: 300 AN: 3348

European-Finnish (FIN) AF: 0.0218 AC: 208 AN: 9548

Middle Eastern (MID) AF: 0.106 AC: 23 AN: 218

European-Non Finnish (NFE) AF: 0.0407 AC: 2308 AN: 56718

Other (OTH) AF: 0.0717 AC: 113 AN: 1576

⚠️ 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: 0.0156 Hom.: 12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.087
DANN	Benign	0.21
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs375385; hg19: chr2-89527895; COSMIC: COSV67689174;