13-80242430-C-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 0.356 in 152,068 control chromosomes in the GnomAD database, including 10,011 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 0.36 ( 10011 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.921
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=-1.02).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 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:
0.356
AC:
54044
AN:
151950
Hom.:
9984
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.446
Gnomad AMI
AF:
0.149
Gnomad AMR
AF:
0.322
Gnomad ASJ
AF:
0.325
Gnomad EAS
AF:
0.228
Gnomad SAS
AF:
0.562
Gnomad FIN
AF:
0.307
Gnomad MID
AF:
0.383
Gnomad NFE
AF:
0.315
Gnomad OTH
AF:
0.349
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.356
AC:
54120
AN:
152068
Hom.:
10011
Cov.:
33
AF XY:
0.359
AC XY:
26660
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.447
Gnomad4 AMR
AF:
0.322
Gnomad4 ASJ
AF:
0.325
Gnomad4 EAS
AF:
0.229
Gnomad4 SAS
AF:
0.560
Gnomad4 FIN
AF:
0.307
Gnomad4 NFE
AF:
0.315
Gnomad4 OTH
AF:
0.352
Alfa
AF:
0.324
Hom.:
16461
Bravo
AF:
0.354
Asia WGS
AF:
0.436
AC:
1517
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.3
DANN
Benign
0.21

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: rs370787; hg19: chr13-80816565; API