12-71935326-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 0.401 in 151,978 control chromosomes in the GnomAD database, including 13,845 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 0.40 ( 13845 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.63

Publications

12 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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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:
0.401
AC:
60866
AN:
151860
Hom.:
13842
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.174
Gnomad AMI
AF:
0.498
Gnomad AMR
AF:
0.484
Gnomad ASJ
AF:
0.489
Gnomad EAS
AF:
0.422
Gnomad SAS
AF:
0.399
Gnomad FIN
AF:
0.538
Gnomad MID
AF:
0.481
Gnomad NFE
AF:
0.490
Gnomad OTH
AF:
0.444
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.401
AC:
60881
AN:
151978
Hom.:
13845
Cov.:
31
AF XY:
0.405
AC XY:
30115
AN XY:
74284
show subpopulations
African (AFR)
AF:
0.174
AC:
7210
AN:
41460
American (AMR)
AF:
0.484
AC:
7391
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.489
AC:
1696
AN:
3470
East Asian (EAS)
AF:
0.422
AC:
2175
AN:
5148
South Asian (SAS)
AF:
0.401
AC:
1925
AN:
4806
European-Finnish (FIN)
AF:
0.538
AC:
5682
AN:
10558
Middle Eastern (MID)
AF:
0.490
AC:
144
AN:
294
European-Non Finnish (NFE)
AF:
0.490
AC:
33274
AN:
67942
Other (OTH)
AF:
0.441
AC:
933
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1688
3376
5065
6753
8441
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
566
1132
1698
2264
2830
<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:
0.435
Hom.:
1900
Bravo
AF:
0.388
Asia WGS
AF:
0.394
AC:
1369
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
1.1
DANN
Benign
0.48
PhyloP100
-1.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs4448731; hg19: chr12-72329106; API