rs9268542

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 0.353 in 152,062 control chromosomes in the GnomAD database, including 10,105 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 0.35 ( 10105 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0970
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=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.485 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:
0.353
AC:
53643
AN:
151942
Hom.:
10098
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.236
Gnomad AMI
AF:
0.348
Gnomad AMR
AF:
0.430
Gnomad ASJ
AF:
0.537
Gnomad EAS
AF:
0.473
Gnomad SAS
AF:
0.501
Gnomad FIN
AF:
0.307
Gnomad MID
AF:
0.596
Gnomad NFE
AF:
0.383
Gnomad OTH
AF:
0.367
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.353
AC:
53664
AN:
152062
Hom.:
10105
Cov.:
32
AF XY:
0.356
AC XY:
26479
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.236
Gnomad4 AMR
AF:
0.430
Gnomad4 ASJ
AF:
0.537
Gnomad4 EAS
AF:
0.474
Gnomad4 SAS
AF:
0.501
Gnomad4 FIN
AF:
0.307
Gnomad4 NFE
AF:
0.383
Gnomad4 OTH
AF:
0.368
Alfa
AF:
0.392
Hom.:
17769
Bravo
AF:
0.357
Asia WGS
AF:
0.436
AC:
1511
AN:
3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
5.5
DANN
Benign
0.71

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: rs9268542; hg19: chr6-32384721; API