rs157224

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.093 in 152,128 control chromosomes in the GnomAD database, including 728 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 0.093 ( 728 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

6 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 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:
0.0930
AC:
14136
AN:
152010
Hom.:
726
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.125
Gnomad AMI
AF:
0.0406
Gnomad AMR
AF:
0.0820
Gnomad ASJ
AF:
0.0875
Gnomad EAS
AF:
0.126
Gnomad SAS
AF:
0.144
Gnomad FIN
AF:
0.0928
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.0705
Gnomad OTH
AF:
0.0989
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0930
AC:
14145
AN:
152128
Hom.:
728
Cov.:
32
AF XY:
0.0953
AC XY:
7088
AN XY:
74390
show subpopulations
African (AFR)
AF:
0.125
AC:
5203
AN:
41468
American (AMR)
AF:
0.0819
AC:
1252
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.0875
AC:
303
AN:
3464
East Asian (EAS)
AF:
0.126
AC:
654
AN:
5172
South Asian (SAS)
AF:
0.144
AC:
695
AN:
4828
European-Finnish (FIN)
AF:
0.0928
AC:
983
AN:
10592
Middle Eastern (MID)
AF:
0.0714
AC:
21
AN:
294
European-Non Finnish (NFE)
AF:
0.0704
AC:
4790
AN:
67992
Other (OTH)
AF:
0.0979
AC:
207
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
658
1316
1974
2632
3290
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
160
320
480
640
800
<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:
0.0760
Hom.:
646
Bravo
AF:
0.0906
Asia WGS
AF:
0.154
AC:
534
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
CADD
Benign
15
DANN
Benign
0.88
PhyloP100
1.1
PromoterAI
-0.088
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs157224; hg19: chr1-29213334; API