rs9468925

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.443 in 152,078 control chromosomes in the GnomAD database, including 15,400 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 0.44 ( 15400 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.422
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -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 = 0.545 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:
0.443
AC:
67272
AN:
151958
Hom.:
15374
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.552
Gnomad AMI
AF:
0.314
Gnomad AMR
AF:
0.479
Gnomad ASJ
AF:
0.352
Gnomad EAS
AF:
0.376
Gnomad SAS
AF:
0.459
Gnomad FIN
AF:
0.494
Gnomad MID
AF:
0.456
Gnomad NFE
AF:
0.370
Gnomad OTH
AF:
0.446
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.443
AC:
67337
AN:
152078
Hom.:
15400
Cov.:
32
AF XY:
0.449
AC XY:
33335
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.551
AC:
0.551406
AN:
0.551406
Gnomad4 AMR
AF:
0.479
AC:
0.479208
AN:
0.479208
Gnomad4 ASJ
AF:
0.352
AC:
0.351788
AN:
0.351788
Gnomad4 EAS
AF:
0.377
AC:
0.377366
AN:
0.377366
Gnomad4 SAS
AF:
0.459
AC:
0.459163
AN:
0.459163
Gnomad4 FIN
AF:
0.494
AC:
0.493837
AN:
0.493837
Gnomad4 NFE
AF:
0.370
AC:
0.370484
AN:
0.370484
Gnomad4 OTH
AF:
0.443
AC:
0.442763
AN:
0.442763
Heterozygous variant carriers
0
1917
3833
5750
7666
9583
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
630
1260
1890
2520
3150
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.396
Hom.:
43087
Bravo
AF:
0.446
Asia WGS
AF:
0.430
AC:
1496
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
3.6
DANN
Benign
0.72

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: rs9468925; hg19: chr6-31258837; API