rs1746825

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 0.659 in 151,992 control chromosomes in the GnomAD database, including 33,727 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 0.66 ( 33727 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0370
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=-0.62).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 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:
0.659
AC:
100132
AN:
151872
Hom.:
33704
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.528
Gnomad AMI
AF:
0.678
Gnomad AMR
AF:
0.688
Gnomad ASJ
AF:
0.680
Gnomad EAS
AF:
0.667
Gnomad SAS
AF:
0.485
Gnomad FIN
AF:
0.775
Gnomad MID
AF:
0.680
Gnomad NFE
AF:
0.725
Gnomad OTH
AF:
0.659
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.659
AC:
100191
AN:
151992
Hom.:
33727
Cov.:
32
AF XY:
0.660
AC XY:
48998
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.528
Gnomad4 AMR
AF:
0.688
Gnomad4 ASJ
AF:
0.680
Gnomad4 EAS
AF:
0.666
Gnomad4 SAS
AF:
0.487
Gnomad4 FIN
AF:
0.775
Gnomad4 NFE
AF:
0.725
Gnomad4 OTH
AF:
0.659
Alfa
AF:
0.693
Hom.:
4584
Bravo
AF:
0.653
Asia WGS
AF:
0.571
AC:
1987
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
CADD
Benign
7.3
DANN
Benign
0.92

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: rs1746825; hg19: chr9-110148556; API