rs12682834

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 0.638 in 517,622 control chromosomes in the GnomAD database, including 107,041 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 0.60 ( 27523 hom., cov: 32)
Exomes 𝑓: 0.66 ( 79518 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.561
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=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 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:
0.596
AC:
90593
AN:
151926
Hom.:
27499
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.484
Gnomad AMI
AF:
0.614
Gnomad AMR
AF:
0.642
Gnomad ASJ
AF:
0.735
Gnomad EAS
AF:
0.705
Gnomad SAS
AF:
0.746
Gnomad FIN
AF:
0.583
Gnomad MID
AF:
0.659
Gnomad NFE
AF:
0.629
Gnomad OTH
AF:
0.614
GnomAD3 exomes
AF:
0.651
AC:
148378
AN:
228042
Hom.:
48885
AF XY:
0.655
AC XY:
82611
AN XY:
126058
show subpopulations
Gnomad AFR exome
AF:
0.472
Gnomad AMR exome
AF:
0.689
Gnomad ASJ exome
AF:
0.733
Gnomad EAS exome
AF:
0.685
Gnomad SAS exome
AF:
0.740
Gnomad FIN exome
AF:
0.591
Gnomad NFE exome
AF:
0.629
Gnomad OTH exome
AF:
0.655
GnomAD4 exome
AF:
0.655
AC:
239570
AN:
365576
Hom.:
79518
Cov.:
0
AF XY:
0.664
AC XY:
139197
AN XY:
209704
show subpopulations
Gnomad4 AFR exome
AF:
0.475
Gnomad4 AMR exome
AF:
0.688
Gnomad4 ASJ exome
AF:
0.731
Gnomad4 EAS exome
AF:
0.686
Gnomad4 SAS exome
AF:
0.737
Gnomad4 FIN exome
AF:
0.600
Gnomad4 NFE exome
AF:
0.630
Gnomad4 OTH exome
AF:
0.646
GnomAD4 genome
AF:
0.596
AC:
90643
AN:
152046
Hom.:
27523
Cov.:
32
AF XY:
0.596
AC XY:
44295
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.484
Gnomad4 AMR
AF:
0.642
Gnomad4 ASJ
AF:
0.735
Gnomad4 EAS
AF:
0.706
Gnomad4 SAS
AF:
0.747
Gnomad4 FIN
AF:
0.583
Gnomad4 NFE
AF:
0.629
Gnomad4 OTH
AF:
0.616
Alfa
AF:
0.634
Hom.:
7025
Bravo
AF:
0.595
Asia WGS
AF:
0.709
AC:
2462
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.38
DANN
Benign
0.28

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: rs12682834; hg19: chr9-90062823; COSMIC: COSV60795570; API