chr20-584433-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 0.148 in 151,934 control chromosomes in the GnomAD database, including 2,579 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 0.15 ( 2579 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.57

Publications

8 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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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:
0.148
AC:
22464
AN:
151816
Hom.:
2573
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.165
Gnomad AMI
AF:
0.189
Gnomad AMR
AF:
0.107
Gnomad ASJ
AF:
0.159
Gnomad EAS
AF:
0.590
Gnomad SAS
AF:
0.459
Gnomad FIN
AF:
0.129
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.0929
Gnomad OTH
AF:
0.150
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.148
AC:
22494
AN:
151934
Hom.:
2579
Cov.:
31
AF XY:
0.157
AC XY:
11640
AN XY:
74274
show subpopulations
African (AFR)
AF:
0.166
AC:
6865
AN:
41454
American (AMR)
AF:
0.108
AC:
1640
AN:
15242
Ashkenazi Jewish (ASJ)
AF:
0.159
AC:
550
AN:
3470
East Asian (EAS)
AF:
0.591
AC:
3029
AN:
5128
South Asian (SAS)
AF:
0.457
AC:
2194
AN:
4796
European-Finnish (FIN)
AF:
0.129
AC:
1360
AN:
10574
Middle Eastern (MID)
AF:
0.170
AC:
50
AN:
294
European-Non Finnish (NFE)
AF:
0.0929
AC:
6316
AN:
67966
Other (OTH)
AF:
0.151
AC:
318
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
862
1724
2585
3447
4309
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
268
536
804
1072
1340
<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:
0.117
Hom.:
5466
Bravo
AF:
0.144
Asia WGS
AF:
0.501
AC:
1739
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.63
DANN
Benign
0.51
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: rs6038071; hg19: chr20-565077; API