rs9820695

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.426 in 152,004 control chromosomes in the GnomAD database, including 15,447 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 0.43 ( 15447 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.161
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.425
AC:
64596
AN:
151886
Hom.:
15395
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.643
Gnomad AMI
AF:
0.224
Gnomad AMR
AF:
0.451
Gnomad ASJ
AF:
0.351
Gnomad EAS
AF:
0.492
Gnomad SAS
AF:
0.476
Gnomad FIN
AF:
0.375
Gnomad MID
AF:
0.484
Gnomad NFE
AF:
0.292
Gnomad OTH
AF:
0.431
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.426
AC:
64715
AN:
152004
Hom.:
15447
Cov.:
32
AF XY:
0.434
AC XY:
32217
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.643
Gnomad4 AMR
AF:
0.451
Gnomad4 ASJ
AF:
0.351
Gnomad4 EAS
AF:
0.491
Gnomad4 SAS
AF:
0.478
Gnomad4 FIN
AF:
0.375
Gnomad4 NFE
AF:
0.292
Gnomad4 OTH
AF:
0.437
Alfa
AF:
0.330
Hom.:
10704
Bravo
AF:
0.441
Asia WGS
AF:
0.544
AC:
1890
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.1
DANN
Benign
0.16

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: rs9820695; hg19: chr3-103331483; API