5-28212616-C-T

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 0.58 in 152,026 control chromosomes in the GnomAD database, including 30,350 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 0.58 ( 30350 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.107

Publications

2 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 = 0.76 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:
0.581
AC:
88271
AN:
151910
Hom.:
30361
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.209
Gnomad AMI
AF:
0.777
Gnomad AMR
AF:
0.619
Gnomad ASJ
AF:
0.755
Gnomad EAS
AF:
0.320
Gnomad SAS
AF:
0.726
Gnomad FIN
AF:
0.765
Gnomad MID
AF:
0.725
Gnomad NFE
AF:
0.766
Gnomad OTH
AF:
0.646
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.580
AC:
88243
AN:
152026
Hom.:
30350
Cov.:
33
AF XY:
0.583
AC XY:
43370
AN XY:
74338
show subpopulations
African (AFR)
AF:
0.208
AC:
8634
AN:
41448
American (AMR)
AF:
0.618
AC:
9442
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.755
AC:
2620
AN:
3470
East Asian (EAS)
AF:
0.320
AC:
1652
AN:
5166
South Asian (SAS)
AF:
0.725
AC:
3498
AN:
4822
European-Finnish (FIN)
AF:
0.765
AC:
8083
AN:
10572
Middle Eastern (MID)
AF:
0.714
AC:
210
AN:
294
European-Non Finnish (NFE)
AF:
0.766
AC:
52048
AN:
67964
Other (OTH)
AF:
0.640
AC:
1347
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1466
2932
4397
5863
7329
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
708
1416
2124
2832
3540
<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:
0.626
Hom.:
7229
Bravo
AF:
0.549
Asia WGS
AF:
0.514
AC:
1771
AN:
3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
3.5
DANN
Benign
0.43
PhyloP100
0.11

Splicing

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

Publications

Other links and lift over

dbSNP: rs7727623; hg19: chr5-28212723; API