Variant chr11-5008473-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 0.561 in 151,884 control chromosomes in the GnomAD database, including 24,434 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 0.56 ( 24434 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.223

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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

85038

AN:

151764

Hom.:

24392

Cov.:

show subpopulations

Gnomad AFR

AF:

0.667

Gnomad AMI

AF:

0.578

Gnomad AMR

AF:

0.566

Gnomad ASJ

AF:

0.586

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.523

Gnomad FIN

AF:

0.519

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.526

Gnomad OTH

AF:

0.569

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

GnomAD4 genome

AF:

0.561

AC:

85140

AN:

151884

Hom.:

24434

Cov.:

AF XY:

0.558

AC XY:

41403

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.667

Gnomad4 AMR

AF:

0.566

Gnomad4 ASJ

AF:

0.586

Gnomad4 EAS

AF:

0.232

Gnomad4 SAS

AF:

0.525

Gnomad4 FIN

AF:

0.519

Gnomad4 NFE

AF:

0.526

Gnomad4 OTH

AF:

0.570

Alfa

AF:

0.530

Hom.:

23044

Bravo

AF:

0.570

Asia WGS

AF:

0.406

AC:

1411

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.3

DANN

Benign

0.41

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