2-146120964-T-C

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 0.943 in 152,248 control chromosomes in the GnomAD database, including 67,951 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 0.94 ( 67951 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.350

Publications

7 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=-1.01).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.976 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:
0.943
AC:
143532
AN:
152130
Hom.:
67921
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.883
Gnomad AMI
AF:
0.926
Gnomad AMR
AF:
0.902
Gnomad ASJ
AF:
0.995
Gnomad EAS
AF:
0.966
Gnomad SAS
AF:
0.910
Gnomad FIN
AF:
0.978
Gnomad MID
AF:
0.949
Gnomad NFE
AF:
0.982
Gnomad OTH
AF:
0.952
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.943
AC:
143619
AN:
152248
Hom.:
67951
Cov.:
33
AF XY:
0.941
AC XY:
70087
AN XY:
74446
show subpopulations
African (AFR)
AF:
0.883
AC:
36669
AN:
41530
American (AMR)
AF:
0.901
AC:
13766
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.995
AC:
3455
AN:
3472
East Asian (EAS)
AF:
0.966
AC:
5003
AN:
5178
South Asian (SAS)
AF:
0.909
AC:
4388
AN:
4826
European-Finnish (FIN)
AF:
0.978
AC:
10381
AN:
10614
Middle Eastern (MID)
AF:
0.946
AC:
278
AN:
294
European-Non Finnish (NFE)
AF:
0.982
AC:
66827
AN:
68032
Other (OTH)
AF:
0.949
AC:
2009
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
402
804
1206
1608
2010
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
912
1824
2736
3648
4560
<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:
0.953
Hom.:
10801
Bravo
AF:
0.935
Asia WGS
AF:
0.920
AC:
3199
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.4
DANN
Benign
0.58
PhyloP100
-0.35

Splicing

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

Publications

Other links and lift over

dbSNP: rs222826; hg19: chr2-146878532; API