rs2388399

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 0.864 in 151,884 control chromosomes in the GnomAD database, including 59,477 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 0.86 ( 59477 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.303
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.982 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:
0.865
AC:
131219
AN:
151766
Hom.:
59453
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.559
Gnomad AMI
AF:
0.990
Gnomad AMR
AF:
0.929
Gnomad ASJ
AF:
0.967
Gnomad EAS
AF:
0.978
Gnomad SAS
AF:
0.991
Gnomad FIN
AF:
0.998
Gnomad MID
AF:
0.918
Gnomad NFE
AF:
0.989
Gnomad OTH
AF:
0.904
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.864
AC:
131293
AN:
151884
Hom.:
59477
Cov.:
31
AF XY:
0.871
AC XY:
64627
AN XY:
74234
show subpopulations
Gnomad4 AFR
AF:
0.559
Gnomad4 AMR
AF:
0.929
Gnomad4 ASJ
AF:
0.967
Gnomad4 EAS
AF:
0.978
Gnomad4 SAS
AF:
0.991
Gnomad4 FIN
AF:
0.998
Gnomad4 NFE
AF:
0.989
Gnomad4 OTH
AF:
0.905
Alfa
AF:
0.910
Hom.:
8841
Bravo
AF:
0.846
Asia WGS
AF:
0.964
AC:
3343
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
3.3
DANN
Benign
0.51

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: rs2388399; hg19: chr10-2792892; API