rs12129861

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 0.423 in 152,008 control chromosomes in the GnomAD database, including 13,968 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 0.42 ( 13968 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0500
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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.423
AC:
64306
AN:
151890
Hom.:
13965
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.387
Gnomad AMI
AF:
0.449
Gnomad AMR
AF:
0.399
Gnomad ASJ
AF:
0.356
Gnomad EAS
AF:
0.185
Gnomad SAS
AF:
0.300
Gnomad FIN
AF:
0.485
Gnomad MID
AF:
0.351
Gnomad NFE
AF:
0.472
Gnomad OTH
AF:
0.411
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.423
AC:
64346
AN:
152008
Hom.:
13968
Cov.:
32
AF XY:
0.422
AC XY:
31304
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.387
Gnomad4 AMR
AF:
0.399
Gnomad4 ASJ
AF:
0.356
Gnomad4 EAS
AF:
0.184
Gnomad4 SAS
AF:
0.301
Gnomad4 FIN
AF:
0.485
Gnomad4 NFE
AF:
0.472
Gnomad4 OTH
AF:
0.407
Alfa
AF:
0.446
Hom.:
25275
Bravo
AF:
0.413
Asia WGS
AF:
0.234
AC:
815
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.6
DANN
Benign
0.46

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: rs12129861; hg19: chr1-145725689; API