chr2-89913792-A-C

Variant names:

• chr2-89913792-A-C
• rs385951

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 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 0.0057 (99 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00571 (585/102428) while in subpopulation AMR AF = 0.0489 (509/10418). AF 95% confidence interval is 0.0454. There are 99 homozygotes in GnomAd4. There are 257 alleles in the male GnomAd4 subpopulation. Median coverage is 19. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 99 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>C		upstream_gene	N/A	ENSP00000374800.2	P01593

Frequencies

GnomAD3 genomes AF: 0.00558 AC: 571 AN: 102390 Hom.: 93 Cov.: 19

Gnomad AFR AF: 0.00381

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000902

Gnomad OTH AF: 0.00472

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

GnomAD4 genome AF: 0.00571 AC: 585 AN: 102428 Hom.: 99 Cov.: 19 AF XY: 0.00516 AC XY: 257 AN XY: 49814

African (AFR) AF: 0.00380 AC: 64 AN: 16834

American (AMR) AF: 0.0489 AC: 509 AN: 10418

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2940

East Asian (EAS) AF: 0.00 AC: 0 AN: 2504

South Asian (SAS) AF: 0.00 AC: 0 AN: 3192

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 222

European-Non Finnish (NFE) AF: 0.0000903 AC: 5 AN: 55400

Other (OTH) AF: 0.00467 AC: 7 AN: 1500

Alfa AF: 0.00 Hom.: 16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.60
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;