Genetic Variant :null (chr11-134602767-T-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is . The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.841 in 152,196 control chromosomes in the GnomAD database, including 53,945 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 0.84 ( 53945 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04

Publications

2 publications found

Variant links:

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ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Variant Effect in Transcripts

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes

AF:

0.841

AC:

127922

AN:

152078

Hom.:

53898

Cov.:

show subpopulations

Gnomad AFR

AF:

0.805

Gnomad AMI

AF:

0.860

Gnomad AMR

AF:

0.868

Gnomad ASJ

AF:

0.847

Gnomad EAS

AF:

0.682

Gnomad SAS

AF:

0.826

Gnomad FIN

AF:

0.885

Gnomad MID

AF:

0.848

Gnomad NFE

AF:

0.863

Gnomad OTH

AF:

0.845

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

GnomAD4 genome

AF:

0.841

AC:

128026

AN:

152196

Hom.:

53945

Cov.:

AF XY:

0.842

AC XY:

62677

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.805

AC:

33433

AN:

41524

American (AMR)

AF:

0.868

AC:

13270

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.847

AC:

2942

AN:

3472

East Asian (EAS)

AF:

0.682

AC:

3527

AN:

5170

South Asian (SAS)

AF:

0.827

AC:

3989

AN:

4824

European-Finnish (FIN)

AF:

0.885

AC:

9376

AN:

10592

Middle Eastern (MID)

AF:

0.844

AC:

248

AN:

294

European-Non Finnish (NFE)

AF:

0.863

AC:

58671

AN:

68002

Other (OTH)

AF:

0.846

AC:

1786

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1046

2092

3139

4185

5231

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.855

Hom.:

6907

Bravo

AF:

0.835

Asia WGS

AF:

0.784

AC:

2726

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over