13-106416281-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.27 in 152,132 control chromosomes in the GnomAD database, including 6,201 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 0.27 ( 6201 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.839
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.270
AC:
41065
AN:
152016
Hom.:
6203
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.393
Gnomad AMI
AF:
0.167
Gnomad AMR
AF:
0.345
Gnomad ASJ
AF:
0.243
Gnomad EAS
AF:
0.298
Gnomad SAS
AF:
0.266
Gnomad FIN
AF:
0.150
Gnomad MID
AF:
0.360
Gnomad NFE
AF:
0.197
Gnomad OTH
AF:
0.296
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.270
AC:
41093
AN:
152132
Hom.:
6201
Cov.:
33
AF XY:
0.269
AC XY:
19987
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.392
Gnomad4 AMR
AF:
0.346
Gnomad4 ASJ
AF:
0.243
Gnomad4 EAS
AF:
0.298
Gnomad4 SAS
AF:
0.265
Gnomad4 FIN
AF:
0.150
Gnomad4 NFE
AF:
0.197
Gnomad4 OTH
AF:
0.294
Alfa
AF:
0.227
Hom.:
5684
Bravo
AF:
0.293
Asia WGS
AF:
0.281
AC:
977
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.33
CADD
Benign
15
DANN
Benign
0.61

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: rs1322740; hg19: chr13-107068629; API