Variant 11-18264227-A-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 0.668 in 152,066 control chromosomes in the GnomAD database, including 34,216 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 0.67 ( 34216 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.06

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 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:

0.668

AC:

101503

AN:

151948

Hom.:

34178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.653

Gnomad AMI

AF:

0.565

Gnomad AMR

AF:

0.604

Gnomad ASJ

AF:

0.518

Gnomad EAS

AF:

0.682

Gnomad SAS

AF:

0.610

Gnomad FIN

AF:

0.755

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.693

Gnomad OTH

AF:

0.610

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

GnomAD4 genome

AF:

0.668

AC:

101593

AN:

152066

Hom.:

34216

Cov.:

AF XY:

0.668

AC XY:

49638

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.653

Gnomad4 AMR

AF:

0.603

Gnomad4 ASJ

AF:

0.518

Gnomad4 EAS

AF:

0.682

Gnomad4 SAS

AF:

0.611

Gnomad4 FIN

AF:

0.755

Gnomad4 NFE

AF:

0.693

Gnomad4 OTH

AF:

0.610

Alfa

AF:

0.514

Hom.:

807

Bravo

AF:

0.656

Asia WGS

AF:

0.701

AC:

2436

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.057

DANN

Benign

0.35

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