chr9-5354681-C-T

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 0.476 in 151,978 control chromosomes in the GnomAD database, including 17,628 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 0.48 ( 17628 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.791
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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:
0.476
AC:
72240
AN:
151860
Hom.:
17608
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.588
Gnomad AMI
AF:
0.269
Gnomad AMR
AF:
0.488
Gnomad ASJ
AF:
0.489
Gnomad EAS
AF:
0.478
Gnomad SAS
AF:
0.473
Gnomad FIN
AF:
0.428
Gnomad MID
AF:
0.554
Gnomad NFE
AF:
0.413
Gnomad OTH
AF:
0.493
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.476
AC:
72309
AN:
151978
Hom.:
17628
Cov.:
32
AF XY:
0.479
AC XY:
35560
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.589
Gnomad4 AMR
AF:
0.487
Gnomad4 ASJ
AF:
0.489
Gnomad4 EAS
AF:
0.478
Gnomad4 SAS
AF:
0.472
Gnomad4 FIN
AF:
0.428
Gnomad4 NFE
AF:
0.413
Gnomad4 OTH
AF:
0.494
Alfa
AF:
0.437
Hom.:
14797
Bravo
AF:
0.485
Asia WGS
AF:
0.523
AC:
1819
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.41
DANN
Benign
0.58

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: rs10815188; hg19: chr9-5354681; API