rs9648058

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 0.0577 in 152,144 control chromosomes in the GnomAD database, including 346 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 0.058 ( 346 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.457
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=-0.73).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0577
AC:
8772
AN:
152026
Hom.:
345
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0123
Gnomad AMI
AF:
0.0956
Gnomad AMR
AF:
0.0592
Gnomad ASJ
AF:
0.112
Gnomad EAS
AF:
0.107
Gnomad SAS
AF:
0.136
Gnomad FIN
AF:
0.0485
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.0731
Gnomad OTH
AF:
0.0730
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0577
AC:
8774
AN:
152144
Hom.:
346
Cov.:
32
AF XY:
0.0593
AC XY:
4409
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.0123
Gnomad4 AMR
AF:
0.0592
Gnomad4 ASJ
AF:
0.112
Gnomad4 EAS
AF:
0.106
Gnomad4 SAS
AF:
0.137
Gnomad4 FIN
AF:
0.0485
Gnomad4 NFE
AF:
0.0731
Gnomad4 OTH
AF:
0.0727
Alfa
AF:
0.0656
Hom.:
65
Bravo
AF:
0.0543
Asia WGS
AF:
0.0990
AC:
345
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
4.1
DANN
Benign
0.74

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: rs9648058; hg19: chr7-38109858; API