GeneBe

chr12-91112087-CT-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.0312 in 152,210 control chromosomes in the GnomAD database, including 248 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.031 ( 248 hom., cov: 32)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.236

Publications

2 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 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:
0.0312
AC:
4738
AN:
152092
Hom.:
247
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0154
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.0396
Gnomad ASJ
AF:
0.0185
Gnomad EAS
AF:
0.261
Gnomad SAS
AF:
0.0908
Gnomad FIN
AF:
0.0198
Gnomad MID
AF:
0.0570
Gnomad NFE
AF:
0.0197
Gnomad OTH
AF:
0.0321
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0312
AC:
4743
AN:
152210
Hom.:
248
Cov.:
32
AF XY:
0.0344
AC XY:
2556
AN XY:
74400
show subpopulations
African (AFR)
AF:
0.0156
AC:
650
AN:
41554
American (AMR)
AF:
0.0395
AC:
603
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.0185
AC:
64
AN:
3468
East Asian (EAS)
AF:
0.261
AC:
1350
AN:
5168
South Asian (SAS)
AF:
0.0911
AC:
439
AN:
4818
European-Finnish (FIN)
AF:
0.0198
AC:
210
AN:
10592
Middle Eastern (MID)
AF:
0.0544
AC:
16
AN:
294
European-Non Finnish (NFE)
AF:
0.0197
AC:
1340
AN:
68016
Other (OTH)
AF:
0.0313
AC:
66
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
210
420
629
839
1049
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
62
124
186
248
310
<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:
0.00907
Hom.:
1
Bravo
AF:
0.0322
Asia WGS
AF:
0.167
AC:
581
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.24

Splicing

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

Publications

Other links and lift over

dbSNP: rs17018757; hg19: chr12-91505864; API