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GeneBe

rs1800587

chr2-112785383-G-Achr2-112785383-G-Cchr2-112785383-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.317 in 151996 control chromosomes in the gnomAD Genomes database, including 7944 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 0.32 ( 7944 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.170

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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:
0.317
AC:
48202
AN:
151996
Hom.:
7944
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.392
Gnomad AMI
AF:
0.407
Gnomad AMR
AF:
0.291
Gnomad ASJ
AF:
0.343
Gnomad EAS
AF:
0.0787
Gnomad SAS
AF:
0.291
Gnomad FIN
AF:
0.316
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.295
Gnomad OTH
AF:
0.308
Alfa
AF:
0.285
Hom.:
6471
Bravo
AF:
0.316
Asia WGS
AF:
0.212
AC:
741
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
2.6
Dann
Benign
0.38

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: rs1800587; hg19: chr2-113542960;