rs3087243

Positions:

• chr2-203874196-G-A
• chr2-203874196-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3 O:2
• Conservation: PhyloP100: -0.151

ACMG classification

Verdict is Benign. Variant got -20 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_multiple_submitters_no_conflicts, 2 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	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56263 AN: 151940 Hom.: 11262 Cov.: 32

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

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:3 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

chronic fatigue syndrome with infection-triggered onset Benign:1

protective, no assertion criteria provided

case-control

Institute for Medical Immunology, Charité - Universitätsmedizin Berlin

Feb 10, 2020

G allele is associated with chronic fatigue syndrome with infection-triggered onset (OR 1.53 [CI 1.17-2.03], p = 0,001) -

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 19, 2024

- -

Hashimoto thyroiditis, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Oct 17, 2011

- -

Celiac disease, susceptibility to, 3 Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Sep 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

Other links and lift over

dbSNP: rs3087243; hg19: chr2-204738919;