2-90115175-C-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000417279.3(IGKV3D-15):​c.120C>A​(p.Thr40Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0012 ( 7 hom., cov: 8)
Exomes 𝑓: 0.0017 ( 131 hom. )
Failed GnomAD Quality Control

Consequence

IGKV3D-15
ENST00000417279.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.299
Variant links:
Genes affected
IGKV3D-15 (HGNC:5824): (immunoglobulin kappa variable 3D-15) Predicted to be involved in immune response. Predicted to be located in plasma membrane. Predicted to be part of immunoglobulin complex. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 2-90115175-C-A is Benign according to our data. Variant chr2-90115175-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2651111.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.299 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IGKV3D-15unassigned_transcript_454 c.120C>A p.Thr40Thr synonymous_variant Exon 2 of 2
IGK n.90115175C>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IGKV3D-15ENST00000417279.3 linkc.120C>A p.Thr40Thr synonymous_variant Exon 2 of 2 6 ENSP00000403672.3 A0A087WSY6

Frequencies

GnomAD3 genomes
AF:
0.00115
AC:
79
AN:
68412
Hom.:
7
Cov.:
8
show subpopulations
Gnomad AFR
AF:
0.000120
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000194
Gnomad ASJ
AF:
0.00253
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000856
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00237
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000949
AC:
71
AN:
74818
Hom.:
2
AF XY:
0.000949
AC XY:
35
AN XY:
36874
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000624
Gnomad ASJ exome
AF:
0.000513
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000777
Gnomad NFE exome
AF:
0.00193
Gnomad OTH exome
AF:
0.000455
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00171
AC:
834
AN:
486936
Hom.:
131
Cov.:
0
AF XY:
0.00179
AC XY:
465
AN XY:
259894
show subpopulations
Gnomad4 AFR exome
AF:
0.0000646
Gnomad4 AMR exome
AF:
0.000706
Gnomad4 ASJ exome
AF:
0.00116
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000393
Gnomad4 FIN exome
AF:
0.00154
Gnomad4 NFE exome
AF:
0.00240
Gnomad4 OTH exome
AF:
0.00187
GnomAD4 genome
AF:
0.00115
AC:
79
AN:
68404
Hom.:
7
Cov.:
8
AF XY:
0.00117
AC XY:
36
AN XY:
30842
show subpopulations
Gnomad4 AFR
AF:
0.000120
Gnomad4 AMR
AF:
0.000194
Gnomad4 ASJ
AF:
0.00253
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000856
Gnomad4 NFE
AF:
0.00237
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00195
Hom.:
2

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jan 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

IGKV2D-28: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
1.9
DANN
Benign
0.26

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs780707382; hg19: chr2-90154033; API