rs12486123

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 0.0874 in 152,126 control chromosomes in the GnomAD database, including 699 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 0.087 ( 699 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.133
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 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:
0.0875
AC:
13299
AN:
152008
Hom.:
699
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0245
Gnomad AMI
AF:
0.0680
Gnomad AMR
AF:
0.104
Gnomad ASJ
AF:
0.113
Gnomad EAS
AF:
0.0434
Gnomad SAS
AF:
0.0669
Gnomad FIN
AF:
0.119
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.120
Gnomad OTH
AF:
0.105
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0874
AC:
13303
AN:
152126
Hom.:
699
Cov.:
32
AF XY:
0.0867
AC XY:
6449
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.0245
Gnomad4 AMR
AF:
0.104
Gnomad4 ASJ
AF:
0.113
Gnomad4 EAS
AF:
0.0431
Gnomad4 SAS
AF:
0.0676
Gnomad4 FIN
AF:
0.119
Gnomad4 NFE
AF:
0.120
Gnomad4 OTH
AF:
0.103
Alfa
AF:
0.108
Hom.:
219
Bravo
AF:
0.0838
Asia WGS
AF:
0.0630
AC:
219
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.96
DANN
Benign
0.71

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: rs12486123; hg19: chr3-30380837; API