rs9310862

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 0.483 in 152,000 control chromosomes in the GnomAD database, including 17,825 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 ( 17825 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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:
0.483
AC:
73340
AN:
151882
Hom.:
17817
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.437
Gnomad AMI
AF:
0.502
Gnomad AMR
AF:
0.483
Gnomad ASJ
AF:
0.510
Gnomad EAS
AF:
0.595
Gnomad SAS
AF:
0.571
Gnomad FIN
AF:
0.448
Gnomad MID
AF:
0.589
Gnomad NFE
AF:
0.498
Gnomad OTH
AF:
0.521
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.483
AC:
73384
AN:
152000
Hom.:
17825
Cov.:
32
AF XY:
0.482
AC XY:
35840
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.437
Gnomad4 AMR
AF:
0.483
Gnomad4 ASJ
AF:
0.510
Gnomad4 EAS
AF:
0.595
Gnomad4 SAS
AF:
0.571
Gnomad4 FIN
AF:
0.448
Gnomad4 NFE
AF:
0.498
Gnomad4 OTH
AF:
0.521
Alfa
AF:
0.493
Hom.:
9773
Bravo
AF:
0.487
Asia WGS
AF:
0.588
AC:
2045
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.085
DANN
Benign
0.41

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: rs9310862; hg19: chr3-28206877; API