rs9657655

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 0.749 in 151,958 control chromosomes in the GnomAD database, including 43,491 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 0.75 ( 43491 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.841
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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 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:
0.749
AC:
113683
AN:
151840
Hom.:
43452
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.596
Gnomad AMI
AF:
0.658
Gnomad AMR
AF:
0.808
Gnomad ASJ
AF:
0.796
Gnomad EAS
AF:
0.979
Gnomad SAS
AF:
0.824
Gnomad FIN
AF:
0.887
Gnomad MID
AF:
0.696
Gnomad NFE
AF:
0.783
Gnomad OTH
AF:
0.749
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.749
AC:
113775
AN:
151958
Hom.:
43491
Cov.:
31
AF XY:
0.756
AC XY:
56126
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.596
Gnomad4 AMR
AF:
0.808
Gnomad4 ASJ
AF:
0.796
Gnomad4 EAS
AF:
0.980
Gnomad4 SAS
AF:
0.824
Gnomad4 FIN
AF:
0.887
Gnomad4 NFE
AF:
0.783
Gnomad4 OTH
AF:
0.752
Alfa
AF:
0.726
Hom.:
2347
Bravo
AF:
0.737
Asia WGS
AF:
0.880
AC:
3048
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.1
DANN
Benign
0.31

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: rs9657655; hg19: chr9-113391486; API