rs590523

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 0.194 in 151,382 control chromosomes in the GnomAD database, including 3,187 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 0.19 ( 3187 hom., cov: 29)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.503
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=-1.0).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.194
AC:
29392
AN:
151264
Hom.:
3186
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.111
Gnomad AMI
AF:
0.248
Gnomad AMR
AF:
0.242
Gnomad ASJ
AF:
0.300
Gnomad EAS
AF:
0.178
Gnomad SAS
AF:
0.118
Gnomad FIN
AF:
0.125
Gnomad MID
AF:
0.252
Gnomad NFE
AF:
0.245
Gnomad OTH
AF:
0.211
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.194
AC:
29409
AN:
151382
Hom.:
3187
Cov.:
29
AF XY:
0.188
AC XY:
13921
AN XY:
73920
show subpopulations
Gnomad4 AFR
AF:
0.111
Gnomad4 AMR
AF:
0.242
Gnomad4 ASJ
AF:
0.300
Gnomad4 EAS
AF:
0.179
Gnomad4 SAS
AF:
0.118
Gnomad4 FIN
AF:
0.125
Gnomad4 NFE
AF:
0.245
Gnomad4 OTH
AF:
0.209
Alfa
AF:
0.211
Hom.:
603
Bravo
AF:
0.205
Asia WGS
AF:
0.153
AC:
531
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.5
DANN
Benign
0.60

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: rs590523; hg19: chr6-137950877; API