13-106145270-T-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 0.0979 in 152,264 control chromosomes in the GnomAD database, including 939 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 0.098 ( 939 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.402
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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 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:
0.0978
AC:
14874
AN:
152146
Hom.:
936
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0842
Gnomad AMI
AF:
0.0757
Gnomad AMR
AF:
0.183
Gnomad ASJ
AF:
0.107
Gnomad EAS
AF:
0.213
Gnomad SAS
AF:
0.162
Gnomad FIN
AF:
0.0506
Gnomad MID
AF:
0.0886
Gnomad NFE
AF:
0.0805
Gnomad OTH
AF:
0.106
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0979
AC:
14902
AN:
152264
Hom.:
939
Cov.:
32
AF XY:
0.0993
AC XY:
7391
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.0847
Gnomad4 AMR
AF:
0.183
Gnomad4 ASJ
AF:
0.107
Gnomad4 EAS
AF:
0.213
Gnomad4 SAS
AF:
0.162
Gnomad4 FIN
AF:
0.0506
Gnomad4 NFE
AF:
0.0805
Gnomad4 OTH
AF:
0.106
Alfa
AF:
0.0608
Hom.:
113
Bravo
AF:
0.112
Asia WGS
AF:
0.173
AC:
601
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.45
DANN
Benign
0.64

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: rs17182039; hg19: chr13-106797619; API