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 rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein 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