20-1944061-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 0.329 in 152,024 control chromosomes in the GnomAD database, including 9,168 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 0.33 ( 9168 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.331

Publications

13 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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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:
0.329
AC:
49935
AN:
151906
Hom.:
9151
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.359
Gnomad AMI
AF:
0.496
Gnomad AMR
AF:
0.353
Gnomad ASJ
AF:
0.319
Gnomad EAS
AF:
0.747
Gnomad SAS
AF:
0.572
Gnomad FIN
AF:
0.222
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.270
Gnomad OTH
AF:
0.351
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.329
AC:
49996
AN:
152024
Hom.:
9168
Cov.:
32
AF XY:
0.335
AC XY:
24861
AN XY:
74306
show subpopulations
African (AFR)
AF:
0.359
AC:
14874
AN:
41438
American (AMR)
AF:
0.353
AC:
5395
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.319
AC:
1106
AN:
3466
East Asian (EAS)
AF:
0.746
AC:
3854
AN:
5166
South Asian (SAS)
AF:
0.573
AC:
2760
AN:
4818
European-Finnish (FIN)
AF:
0.222
AC:
2347
AN:
10566
Middle Eastern (MID)
AF:
0.371
AC:
109
AN:
294
European-Non Finnish (NFE)
AF:
0.270
AC:
18349
AN:
67982
Other (OTH)
AF:
0.356
AC:
752
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
1613
3226
4839
6452
8065
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
504
1008
1512
2016
2520
<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:
0.326
Hom.:
5629
Bravo
AF:
0.341
Asia WGS
AF:
0.666
AC:
2317
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.99
DANN
Benign
0.42
PhyloP100
-0.33

Splicing

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

Publications

Other links and lift over

dbSNP: rs13042885; hg19: chr20-1924707; API