rs232228

Variant names:

• chr2-88859459-G-A
• rs232228

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 0.151 in 148,736 control chromosomes in the GnomAD database, including 2,032 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 0.15 (2032 hom., cov: 33)
• Consequence: IGK intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 1 publications found

Genes affected

IGK (HGNC:5715):

ENSG00000240040 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGK		n.88859459G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000240040	ENST00000624935.3	n.39+2066C>T		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22523 AN: 148676 Hom.: 2029 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.151 AC: 22532 AN: 148736 Hom.: 2032 Cov.: 33 AF XY: 0.152 AC XY: 11040 AN XY: 72442

African (AFR) AF: 0.109 AC: 4429 AN: 40584

American (AMR) AF: 0.246 AC: 3593 AN: 14632

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 601 AN: 3460

East Asian (EAS) AF: 0.306 AC: 1397 AN: 4570

South Asian (SAS) AF: 0.103 AC: 468 AN: 4554

European-Finnish (FIN) AF: 0.107 AC: 1093 AN: 10258

Middle Eastern (MID) AF: 0.165 AC: 37 AN: 224

European-Non Finnish (NFE) AF: 0.154 AC: 10398 AN: 67486

Other (OTH) AF: 0.168 AC: 346 AN: 2056

Alfa AF: 0.136 Hom.: 201

Bravo AF: 0.168

Asia WGS AF: 0.165 AC: 561 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.35
PhyloP100		-0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs232228; hg19: chr2-89158971;