1-186650720-A-G

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 0.991 in 152,252 control chromosomes in the GnomAD database, including 74,807 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 0.99 ( 74807 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.563
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 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:
0.991
AC:
150797
AN:
152134
Hom.:
74751
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.998
Gnomad AMI
AF:
0.975
Gnomad AMR
AF:
0.995
Gnomad ASJ
AF:
0.975
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.947
Gnomad FIN
AF:
0.997
Gnomad MID
AF:
0.956
Gnomad NFE
AF:
0.989
Gnomad OTH
AF:
0.987
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.991
AC:
150912
AN:
152252
Hom.:
74807
Cov.:
32
AF XY:
0.991
AC XY:
73752
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.998
Gnomad4 AMR
AF:
0.995
Gnomad4 ASJ
AF:
0.975
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.946
Gnomad4 FIN
AF:
0.997
Gnomad4 NFE
AF:
0.989
Gnomad4 OTH
AF:
0.987
Alfa
AF:
0.991
Hom.:
9425
Bravo
AF:
0.992
Asia WGS
AF:
0.978
AC:
3399
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.47
DANN
Benign
0.46

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: rs718665; hg19: chr1-186619852; API