rs12128121

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 0.0967 in 152,270 control chromosomes in the GnomAD database, including 851 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 0.097 ( 851 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.60
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=-1.0).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 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:
0.0966
AC:
14694
AN:
152152
Hom.:
846
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0484
Gnomad AMI
AF:
0.0559
Gnomad AMR
AF:
0.179
Gnomad ASJ
AF:
0.0971
Gnomad EAS
AF:
0.0543
Gnomad SAS
AF:
0.150
Gnomad FIN
AF:
0.0949
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.107
Gnomad OTH
AF:
0.106
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0967
AC:
14722
AN:
152270
Hom.:
851
Cov.:
32
AF XY:
0.0995
AC XY:
7407
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.0488
Gnomad4 AMR
AF:
0.179
Gnomad4 ASJ
AF:
0.0971
Gnomad4 EAS
AF:
0.0542
Gnomad4 SAS
AF:
0.151
Gnomad4 FIN
AF:
0.0949
Gnomad4 NFE
AF:
0.107
Gnomad4 OTH
AF:
0.108
Alfa
AF:
0.116
Hom.:
1072
Bravo
AF:
0.102
Asia WGS
AF:
0.115
AC:
400
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.39
DANN
Benign
0.61

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: rs12128121; hg19: chr1-22932162; API