rs1659412

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 0.895 in 152,248 control chromosomes in the GnomAD database, including 61,048 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 0.89 ( 61048 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.126
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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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:
0.895
AC:
136104
AN:
152130
Hom.:
60996
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.859
Gnomad AMI
AF:
0.914
Gnomad AMR
AF:
0.934
Gnomad ASJ
AF:
0.896
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.964
Gnomad FIN
AF:
0.878
Gnomad MID
AF:
0.937
Gnomad NFE
AF:
0.896
Gnomad OTH
AF:
0.920
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.895
AC:
136215
AN:
152248
Hom.:
61048
Cov.:
32
AF XY:
0.897
AC XY:
66781
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.859
Gnomad4 AMR
AF:
0.935
Gnomad4 ASJ
AF:
0.896
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.964
Gnomad4 FIN
AF:
0.878
Gnomad4 NFE
AF:
0.896
Gnomad4 OTH
AF:
0.920
Alfa
AF:
0.899
Hom.:
39049
Bravo
AF:
0.896
Asia WGS
AF:
0.967
AC:
3357
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.53
DANN
Benign
0.52

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: rs1659412; hg19: chr9-87278152; API