rs7744020

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 0.335 in 151,690 control chromosomes in the GnomAD database, including 8,852 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 ( 8852 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.17

Publications

18 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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 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:
0.335
AC:
50775
AN:
151572
Hom.:
8849
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.394
Gnomad AMI
AF:
0.222
Gnomad AMR
AF:
0.368
Gnomad ASJ
AF:
0.378
Gnomad EAS
AF:
0.247
Gnomad SAS
AF:
0.254
Gnomad FIN
AF:
0.259
Gnomad MID
AF:
0.484
Gnomad NFE
AF:
0.314
Gnomad OTH
AF:
0.369
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.335
AC:
50797
AN:
151690
Hom.:
8852
Cov.:
30
AF XY:
0.331
AC XY:
24496
AN XY:
74116
show subpopulations
African (AFR)
AF:
0.394
AC:
16284
AN:
41348
American (AMR)
AF:
0.368
AC:
5622
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.378
AC:
1310
AN:
3464
East Asian (EAS)
AF:
0.246
AC:
1269
AN:
5152
South Asian (SAS)
AF:
0.252
AC:
1208
AN:
4792
European-Finnish (FIN)
AF:
0.259
AC:
2732
AN:
10542
Middle Eastern (MID)
AF:
0.469
AC:
138
AN:
294
European-Non Finnish (NFE)
AF:
0.313
AC:
21265
AN:
67832
Other (OTH)
AF:
0.366
AC:
767
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
1641
3282
4924
6565
8206
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
498
996
1494
1992
2490
<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:
0.315
Hom.:
11688
Bravo
AF:
0.352
Asia WGS
AF:
0.281
AC:
975
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.39
DANN
Benign
0.72
PhyloP100
-2.2

Splicing

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

Publications

Other links and lift over

dbSNP: rs7744020; hg19: chr6-32626130; API