rs2184588

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 0.0885 in 152,126 control chromosomes in the GnomAD database, including 1,105 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 0.088 ( 1105 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.56
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0885
AC:
13446
AN:
152008
Hom.:
1106
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0924
Gnomad AMI
AF:
0.0296
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.0239
Gnomad EAS
AF:
0.472
Gnomad SAS
AF:
0.125
Gnomad FIN
AF:
0.106
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.0447
Gnomad OTH
AF:
0.0871
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0885
AC:
13457
AN:
152126
Hom.:
1105
Cov.:
32
AF XY:
0.0947
AC XY:
7039
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.0922
Gnomad4 AMR
AF:
0.139
Gnomad4 ASJ
AF:
0.0239
Gnomad4 EAS
AF:
0.472
Gnomad4 SAS
AF:
0.124
Gnomad4 FIN
AF:
0.106
Gnomad4 NFE
AF:
0.0447
Gnomad4 OTH
AF:
0.0914
Alfa
AF:
0.0739
Hom.:
330
Bravo
AF:
0.0944
Asia WGS
AF:
0.286
AC:
993
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.4
DANN
Benign
0.63

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: rs2184588; hg19: chr1-89807854; API