Variant 13-90156981-C-T details in Genebe, Genetics Data Aggregator

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 0.659 in 152,034 control chromosomes in the GnomAD database, including 33,311 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 0.66 ( 33311 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.237

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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.7 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:

0.659

AC:

100061

AN:

151918

Hom.:

33264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.696

Gnomad AMI

AF:

0.660

Gnomad AMR

AF:

0.711

Gnomad ASJ

AF:

0.563

Gnomad EAS

AF:

0.433

Gnomad SAS

AF:

0.526

Gnomad FIN

AF:

0.657

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.657

Gnomad OTH

AF:

0.646

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.659

AC:

100163

AN:

152034

Hom.:

33311

Cov.:

AF XY:

0.654

AC XY:

48565

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.696

Gnomad4 AMR

AF:

0.711

Gnomad4 ASJ

AF:

0.563

Gnomad4 EAS

AF:

0.433

Gnomad4 SAS

AF:

0.527

Gnomad4 FIN

AF:

0.657

Gnomad4 NFE

AF:

0.657

Gnomad4 OTH

AF:

0.639

Alfa

AF:

0.651

Hom.:

15793

Bravo

AF:

0.668

Asia WGS

AF:

0.483

AC:

1677

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.63

DANN

Benign

0.72

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over