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GeneBe

rs166230

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 0.81 in 152,030 control chromosomes in the GnomAD database, including 49,976 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 0.81 ( 49976 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.631
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=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.861 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:
0.810
AC:
123029
AN:
151912
Hom.:
49917
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.806
Gnomad AMI
AF:
0.804
Gnomad AMR
AF:
0.873
Gnomad ASJ
AF:
0.816
Gnomad EAS
AF:
0.631
Gnomad SAS
AF:
0.788
Gnomad FIN
AF:
0.808
Gnomad MID
AF:
0.848
Gnomad NFE
AF:
0.813
Gnomad OTH
AF:
0.825
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.810
AC:
123146
AN:
152030
Hom.:
49976
Cov.:
30
AF XY:
0.809
AC XY:
60118
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.806
Gnomad4 AMR
AF:
0.873
Gnomad4 ASJ
AF:
0.816
Gnomad4 EAS
AF:
0.631
Gnomad4 SAS
AF:
0.788
Gnomad4 FIN
AF:
0.808
Gnomad4 NFE
AF:
0.813
Gnomad4 OTH
AF:
0.824
Alfa
AF:
0.816
Hom.:
10270
Bravo
AF:
0.815
Asia WGS
AF:
0.699
AC:
2433
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
1.2
Dann
Benign
0.58

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: rs166230; hg19: chr3-64053207; API