rs12756570

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.0603 in 152,142 control chromosomes in the GnomAD database, including 408 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 0.060 ( 408 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602

Publications

3 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0603
AC:
9173
AN:
152024
Hom.:
407
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0203
Gnomad AMI
AF:
0.0713
Gnomad AMR
AF:
0.0412
Gnomad ASJ
AF:
0.0484
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0419
Gnomad FIN
AF:
0.0987
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0895
Gnomad OTH
AF:
0.0605
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0603
AC:
9173
AN:
152142
Hom.:
408
Cov.:
32
AF XY:
0.0599
AC XY:
4458
AN XY:
74382
show subpopulations
African (AFR)
AF:
0.0204
AC:
846
AN:
41526
American (AMR)
AF:
0.0411
AC:
628
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.0484
AC:
168
AN:
3468
East Asian (EAS)
AF:
0.000386
AC:
2
AN:
5186
South Asian (SAS)
AF:
0.0423
AC:
204
AN:
4822
European-Finnish (FIN)
AF:
0.0987
AC:
1045
AN:
10588
Middle Eastern (MID)
AF:
0.0272
AC:
8
AN:
294
European-Non Finnish (NFE)
AF:
0.0895
AC:
6081
AN:
67976
Other (OTH)
AF:
0.0598
AC:
126
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
433
866
1298
1731
2164
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
106
212
318
424
530
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0763
Hom.:
790
Bravo
AF:
0.0529
Asia WGS
AF:
0.0170
AC:
61
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.44
DANN
Benign
0.20
PhyloP100
-0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12756570; hg19: chr1-158361101; API