rs3093229

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 0.207 in 152,212 control chromosomes in the GnomAD database, including 3,829 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 0.21 ( 3829 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.519
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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.207
AC:
31531
AN:
152094
Hom.:
3819
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.107
Gnomad AMI
AF:
0.259
Gnomad AMR
AF:
0.256
Gnomad ASJ
AF:
0.0755
Gnomad EAS
AF:
0.449
Gnomad SAS
AF:
0.155
Gnomad FIN
AF:
0.323
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.232
Gnomad OTH
AF:
0.191
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.207
AC:
31560
AN:
152212
Hom.:
3829
Cov.:
33
AF XY:
0.212
AC XY:
15765
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.107
Gnomad4 AMR
AF:
0.256
Gnomad4 ASJ
AF:
0.0755
Gnomad4 EAS
AF:
0.448
Gnomad4 SAS
AF:
0.156
Gnomad4 FIN
AF:
0.323
Gnomad4 NFE
AF:
0.232
Gnomad4 OTH
AF:
0.188
Alfa
AF:
0.221
Hom.:
1030
Bravo
AF:
0.205
Asia WGS
AF:
0.297
AC:
1031
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
1.1
DANN
Benign
0.46

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: rs3093229; hg19: chr13-113757826; API