13-83957536-G-C

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 0.0884 in 151,610 control chromosomes in the GnomAD database, including 730 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 0.088 ( 730 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.171
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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:
0.0884
AC:
13398
AN:
151496
Hom.:
730
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.129
Gnomad AMI
AF:
0.0822
Gnomad AMR
AF:
0.0908
Gnomad ASJ
AF:
0.0781
Gnomad EAS
AF:
0.00117
Gnomad SAS
AF:
0.0315
Gnomad FIN
AF:
0.0296
Gnomad MID
AF:
0.103
Gnomad NFE
AF:
0.0838
Gnomad OTH
AF:
0.0876
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0884
AC:
13407
AN:
151610
Hom.:
730
Cov.:
32
AF XY:
0.0855
AC XY:
6329
AN XY:
74050
show subpopulations
Gnomad4 AFR
AF:
0.128
Gnomad4 AMR
AF:
0.0907
Gnomad4 ASJ
AF:
0.0781
Gnomad4 EAS
AF:
0.00117
Gnomad4 SAS
AF:
0.0315
Gnomad4 FIN
AF:
0.0296
Gnomad4 NFE
AF:
0.0839
Gnomad4 OTH
AF:
0.0867
Alfa
AF:
0.0776
Hom.:
59
Bravo
AF:
0.0970
Asia WGS
AF:
0.0200
AC:
71
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.34
DANN
Benign
0.69

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: rs9319006; hg19: chr13-84531671; API