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GeneBe

rs187084

chr3-52227015-A-Gchr3-52227015-A-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 0.378 in 152014 control chromosomes in the gnomAD Genomes database, including 11156 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 0.38 ( 11156 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.477

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 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:
0.378
AC:
57423
AN:
152014
Hom.:
11156
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.302
Gnomad AMI
AF:
0.456
Gnomad AMR
AF:
0.430
Gnomad ASJ
AF:
0.408
Gnomad EAS
AF:
0.393
Gnomad SAS
AF:
0.350
Gnomad FIN
AF:
0.422
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.404
Gnomad OTH
AF:
0.365
Alfa
AF:
0.401
Hom.:
12450
Bravo
AF:
0.375
Asia WGS
AF:
0.395
AC:
1373
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
1.3
Dann
Benign
0.36

Splicing

Find out SpliceAI 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: rs187084; hg19: chr3-52261031;