rs1358594

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 0.798 in 151,910 control chromosomes in the GnomAD database, including 51,439 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 0.80 ( 51439 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.447
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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.934 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:
0.799
AC:
121253
AN:
151792
Hom.:
51434
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.498
Gnomad AMI
AF:
0.933
Gnomad AMR
AF:
0.894
Gnomad ASJ
AF:
0.869
Gnomad EAS
AF:
0.675
Gnomad SAS
AF:
0.756
Gnomad FIN
AF:
0.965
Gnomad MID
AF:
0.832
Gnomad NFE
AF:
0.940
Gnomad OTH
AF:
0.813
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.798
AC:
121277
AN:
151910
Hom.:
51439
Cov.:
31
AF XY:
0.800
AC XY:
59372
AN XY:
74248
show subpopulations
Gnomad4 AFR
AF:
0.497
Gnomad4 AMR
AF:
0.894
Gnomad4 ASJ
AF:
0.869
Gnomad4 EAS
AF:
0.675
Gnomad4 SAS
AF:
0.756
Gnomad4 FIN
AF:
0.965
Gnomad4 NFE
AF:
0.940
Gnomad4 OTH
AF:
0.808
Alfa
AF:
0.914
Hom.:
127279
Bravo
AF:
0.780
Asia WGS
AF:
0.723
AC:
2515
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.72
DANN
Benign
0.35

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: rs1358594; hg19: chr4-74555477; API