rs8106239

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 0.23 in 152,034 control chromosomes in the GnomAD database, including 4,245 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 0.23 ( 4245 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.181
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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:
0.230
AC:
34925
AN:
151916
Hom.:
4245
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.236
Gnomad AMI
AF:
0.101
Gnomad AMR
AF:
0.323
Gnomad ASJ
AF:
0.160
Gnomad EAS
AF:
0.336
Gnomad SAS
AF:
0.0766
Gnomad FIN
AF:
0.142
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.227
Gnomad OTH
AF:
0.240
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.230
AC:
34930
AN:
152034
Hom.:
4245
Cov.:
31
AF XY:
0.226
AC XY:
16773
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.236
AC:
0.235982
AN:
0.235982
Gnomad4 AMR
AF:
0.323
AC:
0.323329
AN:
0.323329
Gnomad4 ASJ
AF:
0.160
AC:
0.159838
AN:
0.159838
Gnomad4 EAS
AF:
0.336
AC:
0.33572
AN:
0.33572
Gnomad4 SAS
AF:
0.0757
AC:
0.0756633
AN:
0.0756633
Gnomad4 FIN
AF:
0.142
AC:
0.141588
AN:
0.141588
Gnomad4 NFE
AF:
0.227
AC:
0.226543
AN:
0.226543
Gnomad4 OTH
AF:
0.238
AC:
0.237666
AN:
0.237666
Heterozygous variant carriers
0
1341
2682
4022
5363
6704
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
356
712
1068
1424
1780
<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:
0.215
Hom.:
1824
Bravo
AF:
0.249
Asia WGS
AF:
0.179
AC:
623
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.1
DANN
Benign
0.38

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8106239; hg19: chr19-36085358; API