rs583973

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 0.326 in 152,008 control chromosomes in the GnomAD database, including 9,554 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 0.33 ( 9554 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.380
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=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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:
0.326
AC:
49556
AN:
151890
Hom.:
9558
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.158
Gnomad AMI
AF:
0.480
Gnomad AMR
AF:
0.333
Gnomad ASJ
AF:
0.417
Gnomad EAS
AF:
0.0354
Gnomad SAS
AF:
0.168
Gnomad FIN
AF:
0.338
Gnomad MID
AF:
0.332
Gnomad NFE
AF:
0.452
Gnomad OTH
AF:
0.344
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.326
AC:
49550
AN:
152008
Hom.:
9554
Cov.:
32
AF XY:
0.316
AC XY:
23444
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.157
Gnomad4 AMR
AF:
0.333
Gnomad4 ASJ
AF:
0.417
Gnomad4 EAS
AF:
0.0355
Gnomad4 SAS
AF:
0.168
Gnomad4 FIN
AF:
0.338
Gnomad4 NFE
AF:
0.452
Gnomad4 OTH
AF:
0.340
Alfa
AF:
0.421
Hom.:
18717
Bravo
AF:
0.322
Asia WGS
AF:
0.110
AC:
388
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.88
DANN
Benign
0.44

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: rs583973; hg19: chr9-108418212; API