rs12590429

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 0.0717 in 152,190 control chromosomes in the GnomAD database, including 489 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 0.072 ( 489 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54
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=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 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:
0.0717
AC:
10896
AN:
152072
Hom.:
480
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0365
Gnomad AMI
AF:
0.0252
Gnomad AMR
AF:
0.0617
Gnomad ASJ
AF:
0.0755
Gnomad EAS
AF:
0.0544
Gnomad SAS
AF:
0.141
Gnomad FIN
AF:
0.140
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.0807
Gnomad OTH
AF:
0.0837
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0717
AC:
10913
AN:
152190
Hom.:
489
Cov.:
32
AF XY:
0.0749
AC XY:
5572
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.0366
Gnomad4 AMR
AF:
0.0616
Gnomad4 ASJ
AF:
0.0755
Gnomad4 EAS
AF:
0.0541
Gnomad4 SAS
AF:
0.140
Gnomad4 FIN
AF:
0.140
Gnomad4 NFE
AF:
0.0807
Gnomad4 OTH
AF:
0.0918
Alfa
AF:
0.0752
Hom.:
111
Bravo
AF:
0.0625
Asia WGS
AF:
0.106
AC:
370
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.10
DANN
Benign
0.50

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: rs12590429; hg19: chr14-23482940; API