rs9294536

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 0.389 in 151,982 control chromosomes in the GnomAD database, including 12,319 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 0.39 ( 12319 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.570
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=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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:
0.388
AC:
58988
AN:
151866
Hom.:
12294
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.551
Gnomad AMI
AF:
0.378
Gnomad AMR
AF:
0.290
Gnomad ASJ
AF:
0.377
Gnomad EAS
AF:
0.147
Gnomad SAS
AF:
0.272
Gnomad FIN
AF:
0.332
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.347
Gnomad OTH
AF:
0.395
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.389
AC:
59058
AN:
151982
Hom.:
12319
Cov.:
32
AF XY:
0.384
AC XY:
28508
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.552
Gnomad4 AMR
AF:
0.290
Gnomad4 ASJ
AF:
0.377
Gnomad4 EAS
AF:
0.148
Gnomad4 SAS
AF:
0.272
Gnomad4 FIN
AF:
0.332
Gnomad4 NFE
AF:
0.347
Gnomad4 OTH
AF:
0.396
Alfa
AF:
0.353
Hom.:
14407
Bravo
AF:
0.392
Asia WGS
AF:
0.279
AC:
965
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
10
DANN
Benign
0.44

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: rs9294536; hg19: chr6-93520257; API