rs12132178

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 0.477 in 151,950 control chromosomes in the GnomAD database, including 18,099 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 0.48 ( 18099 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.50
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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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:
0.477
AC:
72413
AN:
151832
Hom.:
18092
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.343
Gnomad AMI
AF:
0.652
Gnomad AMR
AF:
0.459
Gnomad ASJ
AF:
0.636
Gnomad EAS
AF:
0.388
Gnomad SAS
AF:
0.538
Gnomad FIN
AF:
0.438
Gnomad MID
AF:
0.636
Gnomad NFE
AF:
0.559
Gnomad OTH
AF:
0.493
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.477
AC:
72457
AN:
151950
Hom.:
18099
Cov.:
31
AF XY:
0.472
AC XY:
35083
AN XY:
74252
show subpopulations
Gnomad4 AFR
AF:
0.343
Gnomad4 AMR
AF:
0.458
Gnomad4 ASJ
AF:
0.636
Gnomad4 EAS
AF:
0.388
Gnomad4 SAS
AF:
0.539
Gnomad4 FIN
AF:
0.438
Gnomad4 NFE
AF:
0.559
Gnomad4 OTH
AF:
0.493
Alfa
AF:
0.536
Hom.:
11025
Bravo
AF:
0.467
Asia WGS
AF:
0.447
AC:
1554
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
4.7
DANN
Benign
0.66

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: rs12132178; hg19: chr1-101272402; API