1-153349108-G-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 0.83 in 152,194 control chromosomes in the GnomAD database, including 52,610 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 0.83 ( 52610 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.294
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 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:
0.830
AC:
126239
AN:
152076
Hom.:
52583
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.757
Gnomad AMI
AF:
0.862
Gnomad AMR
AF:
0.849
Gnomad ASJ
AF:
0.843
Gnomad EAS
AF:
0.878
Gnomad SAS
AF:
0.838
Gnomad FIN
AF:
0.891
Gnomad MID
AF:
0.867
Gnomad NFE
AF:
0.855
Gnomad OTH
AF:
0.836
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.830
AC:
126319
AN:
152194
Hom.:
52610
Cov.:
32
AF XY:
0.833
AC XY:
61977
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.757
Gnomad4 AMR
AF:
0.849
Gnomad4 ASJ
AF:
0.843
Gnomad4 EAS
AF:
0.878
Gnomad4 SAS
AF:
0.838
Gnomad4 FIN
AF:
0.891
Gnomad4 NFE
AF:
0.855
Gnomad4 OTH
AF:
0.837
Alfa
AF:
0.847
Hom.:
24468
Bravo
AF:
0.822
Asia WGS
AF:
0.846
AC:
2944
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.3
DANN
Benign
0.62

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: rs3014864; hg19: chr1-153321584; API