13-27789305-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 0.472 in 152,052 control chromosomes in the GnomAD database, including 17,125 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 0.47 ( 17125 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0540
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=-0.81).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 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:
0.472
AC:
71688
AN:
151934
Hom.:
17107
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.426
Gnomad AMI
AF:
0.307
Gnomad AMR
AF:
0.541
Gnomad ASJ
AF:
0.455
Gnomad EAS
AF:
0.466
Gnomad SAS
AF:
0.653
Gnomad FIN
AF:
0.492
Gnomad MID
AF:
0.475
Gnomad NFE
AF:
0.471
Gnomad OTH
AF:
0.484
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.472
AC:
71767
AN:
152052
Hom.:
17125
Cov.:
33
AF XY:
0.479
AC XY:
35564
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.426
Gnomad4 AMR
AF:
0.542
Gnomad4 ASJ
AF:
0.455
Gnomad4 EAS
AF:
0.467
Gnomad4 SAS
AF:
0.652
Gnomad4 FIN
AF:
0.492
Gnomad4 NFE
AF:
0.471
Gnomad4 OTH
AF:
0.489
Alfa
AF:
0.467
Hom.:
13160
Bravo
AF:
0.469
Asia WGS
AF:
0.575
AC:
2002
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
6.8
DANN
Benign
0.70

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: rs1231054; hg19: chr13-28363442; API