GeneBe

rs242

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.073 in 152,192 control chromosomes in the GnomAD database, including 500 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.073 ( 500 hom., cov: 31)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0980

Publications

8 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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:
0.0730
AC:
11105
AN:
152076
Hom.:
500
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0192
Gnomad AMI
AF:
0.0967
Gnomad AMR
AF:
0.0567
Gnomad ASJ
AF:
0.0853
Gnomad EAS
AF:
0.0564
Gnomad SAS
AF:
0.0692
Gnomad FIN
AF:
0.0974
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.107
Gnomad OTH
AF:
0.0641
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0730
AC:
11108
AN:
152192
Hom.:
500
Cov.:
31
AF XY:
0.0720
AC XY:
5357
AN XY:
74404
show subpopulations
African (AFR)
AF:
0.0192
AC:
798
AN:
41554
American (AMR)
AF:
0.0566
AC:
865
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.0853
AC:
296
AN:
3472
East Asian (EAS)
AF:
0.0564
AC:
291
AN:
5162
South Asian (SAS)
AF:
0.0694
AC:
335
AN:
4824
European-Finnish (FIN)
AF:
0.0974
AC:
1032
AN:
10592
Middle Eastern (MID)
AF:
0.0306
AC:
9
AN:
294
European-Non Finnish (NFE)
AF:
0.107
AC:
7260
AN:
67984
Other (OTH)
AF:
0.0634
AC:
134
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
530
1060
1591
2121
2651
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
136
272
408
544
680
<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:
0.0281
Hom.:
28
Bravo
AF:
0.0675
Asia WGS
AF:
0.0460
AC:
162
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.098

Splicing

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

Publications

Other links and lift over

dbSNP: rs242; hg19: chr1-20869460; API