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GeneBe

rs889312

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.682 in 151,942 control chromosomes in the GnomAD database, including 35,558 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 0.68 ( 35558 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 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:
0.682
AC:
103504
AN:
151824
Hom.:
35543
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.666
Gnomad AMI
AF:
0.672
Gnomad AMR
AF:
0.611
Gnomad ASJ
AF:
0.682
Gnomad EAS
AF:
0.450
Gnomad SAS
AF:
0.612
Gnomad FIN
AF:
0.767
Gnomad MID
AF:
0.671
Gnomad NFE
AF:
0.717
Gnomad OTH
AF:
0.673
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.682
AC:
103549
AN:
151942
Hom.:
35558
Cov.:
31
AF XY:
0.678
AC XY:
50338
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.665
Gnomad4 AMR
AF:
0.610
Gnomad4 ASJ
AF:
0.682
Gnomad4 EAS
AF:
0.450
Gnomad4 SAS
AF:
0.612
Gnomad4 FIN
AF:
0.767
Gnomad4 NFE
AF:
0.717
Gnomad4 OTH
AF:
0.669
Alfa
AF:
0.698
Hom.:
76889
Bravo
AF:
0.668
Asia WGS
AF:
0.548
AC:
1904
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
Cadd
Benign
18
Dann
Benign
0.79

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: rs889312; hg19: chr5-56031884; API