dbSNP rs375160: IGK:n.89170576G>A (chr2-89170576-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

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

The variant allele was found at a frequency of 0.00315 in 150,882 control chromosomes in the GnomAD database, including 1 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 0.0032 ( 1 hom., cov: 27)

Consequence

IGK
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00100

Publications

1 publications found

Variant links:

Genes affected

IGK (HGNC:5715):

IGK links:

IGKV1-22 (HGNC:5734): (immunoglobulin kappa variable 1-22 (pseudogene))

IGKV1-22 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGK		n.89170576G>A		intragenic_variant
IGKV1-22	unassigned_transcript_409	c.*169C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGKV1-22	ENST00000524313.1 link	n.*199C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.00316

AC:

476

AN:

150760

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000269

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00140

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00101

Gnomad SAS

AF:

0.000422

Gnomad FIN

AF:

0.0194

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00327

Gnomad OTH

AF:

0.00385

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

GnomAD4 genome

AF:

0.00315

AC:

476

AN:

150882

Hom.:

Cov.:

AF XY:

0.00369

AC XY:

272

AN XY:

73652

show subpopulations

African (AFR)

AF:

0.000268

AC:

AN:

41072

American (AMR)

AF:

0.00140

AC:

AN:

15046

Ashkenazi Jewish (ASJ)

AF:

0.000577

AC:

AN:

3466

East Asian (EAS)

AF:

0.00102

AC:

AN:

4922

South Asian (SAS)

AF:

0.000422

AC:

AN:

4734

European-Finnish (FIN)

AF:

0.0194

AC:

205

AN:

10564

Middle Eastern (MID)

AF:

0.00

AC:

AN:

264

European-Non Finnish (NFE)

AF:

0.00327

AC:

222

AN:

67804

Other (OTH)

AF:

0.00381

AC:

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.407

Heterozygous variant carriers

118

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00623

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.8

(source)

DANN

Benign

0.51

PhyloP100

-0.0010

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over