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GeneBe

rs187084

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 152,132 control chromosomes in the GnomAD database, including 11,169 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 ( 11169 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.477
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 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
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.378
AC:
57464
AN:
152132
Hom.:
11169
Cov.:
33
AF XY:
0.379
AC XY:
28156
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.302
Gnomad4 AMR
AF:
0.429
Gnomad4 ASJ
AF:
0.408
Gnomad4 EAS
AF:
0.393
Gnomad4 SAS
AF:
0.351
Gnomad4 FIN
AF:
0.422
Gnomad4 NFE
AF:
0.404
Gnomad4 OTH
AF:
0.369
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
0.94
Dann
Benign
0.36

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: rs187084; hg19: chr3-52261031; API