1-115594189-C-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 0.585 in 151,868 control chromosomes in the GnomAD database, including 31,262 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 0.59 ( 31262 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.365
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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:
0.585
AC:
88845
AN:
151750
Hom.:
31264
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.173
Gnomad AMI
AF:
0.867
Gnomad AMR
AF:
0.673
Gnomad ASJ
AF:
0.777
Gnomad EAS
AF:
0.652
Gnomad SAS
AF:
0.535
Gnomad FIN
AF:
0.687
Gnomad MID
AF:
0.769
Gnomad NFE
AF:
0.784
Gnomad OTH
AF:
0.623
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.585
AC:
88849
AN:
151868
Hom.:
31262
Cov.:
30
AF XY:
0.581
AC XY:
43087
AN XY:
74188
show subpopulations
Gnomad4 AFR
AF:
0.172
Gnomad4 AMR
AF:
0.673
Gnomad4 ASJ
AF:
0.777
Gnomad4 EAS
AF:
0.652
Gnomad4 SAS
AF:
0.536
Gnomad4 FIN
AF:
0.687
Gnomad4 NFE
AF:
0.784
Gnomad4 OTH
AF:
0.625
Alfa
AF:
0.749
Hom.:
54987
Bravo
AF:
0.571
Asia WGS
AF:
0.560
AC:
1949
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.9
DANN
Benign
0.67

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: rs3860222; hg19: chr1-116136810; API