Variant 11-13262564-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 0.271 in 152,078 control chromosomes in the GnomAD database, including 5,752 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 ( 5752 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.553

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=-0.68).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 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:

0.271

AC:

41209

AN:

151960

Hom.:

5749

Cov.:

show subpopulations

Gnomad AFR

AF:

0.221

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.325

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.464

Gnomad SAS

AF:

0.308

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.273

Gnomad OTH

AF:

0.251

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

GnomAD4 genome

AF:

0.271

AC:

41227

AN:

152078

Hom.:

5752

Cov.:

AF XY:

0.272

AC XY:

20186

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.221

Gnomad4 AMR

AF:

0.325

Gnomad4 ASJ

AF:

0.262

Gnomad4 EAS

AF:

0.464

Gnomad4 SAS

AF:

0.305

Gnomad4 FIN

AF:

0.265

Gnomad4 NFE

AF:

0.273

Gnomad4 OTH

AF:

0.250

Alfa

AF:

0.244

Hom.:

2229

Bravo

AF:

0.270

Asia WGS

AF:

0.357

AC:

1243

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

5.0

DANN

Benign

0.82

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