rs9405890

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 0.355 in 152,086 control chromosomes in the GnomAD database, including 10,396 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 0.36 ( 10396 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.19
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=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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:
0.355
AC:
53994
AN:
151968
Hom.:
10384
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.504
Gnomad AMI
AF:
0.422
Gnomad AMR
AF:
0.313
Gnomad ASJ
AF:
0.278
Gnomad EAS
AF:
0.283
Gnomad SAS
AF:
0.332
Gnomad FIN
AF:
0.289
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.296
Gnomad OTH
AF:
0.349
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.355
AC:
54032
AN:
152086
Hom.:
10396
Cov.:
32
AF XY:
0.352
AC XY:
26164
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.504
Gnomad4 AMR
AF:
0.313
Gnomad4 ASJ
AF:
0.278
Gnomad4 EAS
AF:
0.283
Gnomad4 SAS
AF:
0.331
Gnomad4 FIN
AF:
0.289
Gnomad4 NFE
AF:
0.296
Gnomad4 OTH
AF:
0.349
Alfa
AF:
0.302
Hom.:
1517
Bravo
AF:
0.363
Asia WGS
AF:
0.327
AC:
1135
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
7.4
DANN
Benign
0.78

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: rs9405890; hg19: chr6-6012721; API