rs3923037

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 0.419 in 152,102 control chromosomes in the GnomAD database, including 14,131 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 0.42 ( 14131 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.165
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 (EAS) allele frequency at 95% confidence interval = 0.828 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:
0.419
AC:
63664
AN:
151984
Hom.:
14125
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.462
Gnomad AMI
AF:
0.443
Gnomad AMR
AF:
0.387
Gnomad ASJ
AF:
0.431
Gnomad EAS
AF:
0.849
Gnomad SAS
AF:
0.598
Gnomad FIN
AF:
0.370
Gnomad MID
AF:
0.589
Gnomad NFE
AF:
0.360
Gnomad OTH
AF:
0.420
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.419
AC:
63702
AN:
152102
Hom.:
14131
Cov.:
33
AF XY:
0.423
AC XY:
31480
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.462
Gnomad4 AMR
AF:
0.386
Gnomad4 ASJ
AF:
0.431
Gnomad4 EAS
AF:
0.849
Gnomad4 SAS
AF:
0.597
Gnomad4 FIN
AF:
0.370
Gnomad4 NFE
AF:
0.360
Gnomad4 OTH
AF:
0.425
Alfa
AF:
0.357
Hom.:
4294
Bravo
AF:
0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.9
DANN
Benign
0.65

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: rs3923037; hg19: chr2-21148274; API