rs2423292

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 0.286 in 152,000 control chromosomes in the GnomAD database, including 6,507 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 0.29 ( 6507 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05
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=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 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:
0.286
AC:
43405
AN:
151882
Hom.:
6484
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.328
Gnomad AMI
AF:
0.276
Gnomad AMR
AF:
0.303
Gnomad ASJ
AF:
0.338
Gnomad EAS
AF:
0.325
Gnomad SAS
AF:
0.487
Gnomad FIN
AF:
0.205
Gnomad MID
AF:
0.297
Gnomad NFE
AF:
0.248
Gnomad OTH
AF:
0.304
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.286
AC:
43474
AN:
152000
Hom.:
6507
Cov.:
32
AF XY:
0.286
AC XY:
21243
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.329
Gnomad4 AMR
AF:
0.303
Gnomad4 ASJ
AF:
0.338
Gnomad4 EAS
AF:
0.325
Gnomad4 SAS
AF:
0.486
Gnomad4 FIN
AF:
0.205
Gnomad4 NFE
AF:
0.248
Gnomad4 OTH
AF:
0.312
Alfa
AF:
0.263
Hom.:
1267
Bravo
AF:
0.294
Asia WGS
AF:
0.442
AC:
1525
AN:
3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.24
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: rs2423292; hg19: chr20-7819432; API