GeneBe

chr2-89228414-A-G

Variant names:

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.646

Publications

2 publications found
Variant links:
Genes affected

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=-1.12).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IGK n.89228414A>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0794
AC:
8460
AN:
106500
Hom.:
867
Cov.:
26
show subpopulations
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
show subpopulations
⚠️ 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.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.279
Heterozygous variant carriers
0
657
1314
1970
2627
3284
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
76
152
228
304
380
<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:
0.0156
Hom.:
12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

Other links and lift over

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