1-58599895-A-T

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 0.472 in 150,930 control chromosomes in the GnomAD database, including 17,955 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 0.47 ( 17955 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.187
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=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 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:
0.472
AC:
71216
AN:
150818
Hom.:
17935
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.640
Gnomad AMI
AF:
0.188
Gnomad AMR
AF:
0.491
Gnomad ASJ
AF:
0.364
Gnomad EAS
AF:
0.512
Gnomad SAS
AF:
0.422
Gnomad FIN
AF:
0.492
Gnomad MID
AF:
0.268
Gnomad NFE
AF:
0.376
Gnomad OTH
AF:
0.426
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.472
AC:
71278
AN:
150930
Hom.:
17955
Cov.:
30
AF XY:
0.476
AC XY:
35037
AN XY:
73662
show subpopulations
Gnomad4 AFR
AF:
0.640
Gnomad4 AMR
AF:
0.491
Gnomad4 ASJ
AF:
0.364
Gnomad4 EAS
AF:
0.512
Gnomad4 SAS
AF:
0.420
Gnomad4 FIN
AF:
0.492
Gnomad4 NFE
AF:
0.375
Gnomad4 OTH
AF:
0.429
Alfa
AF:
0.285
Hom.:
703
Bravo
AF:
0.478
Asia WGS
AF:
0.538
AC:
1864
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
1.5
DANN
Benign
0.80

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: rs107399; hg19: chr1-59065567; API