Menu
GeneBe

rs3087243

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The variant allele was found at a frequency of 0.37 in 152,058 control chromosomes in the GnomAD database, including 11,260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.37 ( 11260 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:2O:2

Conservation

PhyloP100: -0.151
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 2-203874196-G-A is Benign according to our data. Variant chr2-203874196-G-A is described in ClinVar as [Benign]. Clinvar id is 16922.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.370
AC:
56263
AN:
151940
Hom.:
11262
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.229
Gnomad AMI
AF:
0.424
Gnomad AMR
AF:
0.413
Gnomad ASJ
AF:
0.500
Gnomad EAS
AF:
0.245
Gnomad SAS
AF:
0.608
Gnomad FIN
AF:
0.314
Gnomad MID
AF:
0.538
Gnomad NFE
AF:
0.439
Gnomad OTH
AF:
0.428
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.370
AC:
56261
AN:
152058
Hom.:
11260
Cov.:
32
AF XY:
0.368
AC XY:
27352
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.228
Gnomad4 AMR
AF:
0.412
Gnomad4 ASJ
AF:
0.500
Gnomad4 EAS
AF:
0.245
Gnomad4 SAS
AF:
0.606
Gnomad4 FIN
AF:
0.314
Gnomad4 NFE
AF:
0.439
Gnomad4 OTH
AF:
0.430
Alfa
AF:
0.437
Hom.:
26987
Bravo
AF:
0.366
Asia WGS
AF:
0.444
AC:
1542
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:2Other:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

chronic fatigue syndrome with infection-triggered onset Benign:1
protective, no assertion criteria providedcase-controlInstitute for Medical Immunology, Charité - Universitätsmedizin BerlinFeb 10, 2020G allele is associated with chronic fatigue syndrome with infection-triggered onset (OR 1.53 [CI 1.17-2.03], p = 0,001) -
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsuffiency Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 19, 2024- -
Hashimoto thyroiditis, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMOct 17, 2011- -
Celiac disease, susceptibility to, 3 Other:1
risk factor, no assertion criteria providedliterature onlyOMIMSep 01, 2004- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
1.9
Dann
Benign
0.47

Splicing

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: rs3087243; hg19: chr2-204738919; API