Variant 11-118359549-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 0.179 in 152,110 control chromosomes in the GnomAD database, including 2,962 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 0.18 ( 2962 hom., cov: 32)

Exomes 𝑓: 0.10 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.397

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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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:

0.179

AC:

27134

AN:

151942

Hom.:

2969

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.507

Gnomad SAS

AF:

0.467

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.170

GnomAD4 exome

AF:

0.100

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0833

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.105

GnomAD4 genome

AF:

0.179

AC:

27151

AN:

152060

Hom.:

2962

Cov.:

AF XY:

0.187

AC XY:

13892

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.159

Gnomad4 AMR

AF:

0.123

Gnomad4 ASJ

AF:

0.232

Gnomad4 EAS

AF:

0.507

Gnomad4 SAS

AF:

0.465

Gnomad4 FIN

AF:

0.189

Gnomad4 NFE

AF:

0.154

Gnomad4 OTH

AF:

0.173

Alfa

AF:

0.0765

Hom.:

Bravo

AF:

0.168

Asia WGS

AF:

0.449

AC:

1559

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.8

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