Genetic Variant :null (chr2-20934123-A-G) – 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 0.933 in 152,320 control chromosomes in the GnomAD database, including 66,492 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 0.93 ( 66492 hom., cov: 34)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.07

Publications

14 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=-0.37).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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:

0.933

AC:

142034

AN:

152202

Hom.:

66429

Cov.:

show subpopulations

Gnomad AFR

AF:

0.981

Gnomad AMI

AF:

0.661

Gnomad AMR

AF:

0.944

Gnomad ASJ

AF:

0.961

Gnomad EAS

AF:

0.997

Gnomad SAS

AF:

0.903

Gnomad FIN

AF:

0.920

Gnomad MID

AF:

0.968

Gnomad NFE

AF:

0.902

Gnomad OTH

AF:

0.954

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

GnomAD4 genome

AF:

0.933

AC:

142156

AN:

152320

Hom.:

66492

Cov.:

AF XY:

0.934

AC XY:

69529

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.981

AC:

40808

AN:

41578

American (AMR)

AF:

0.944

AC:

14448

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.961

AC:

3335

AN:

3472

East Asian (EAS)

AF:

0.997

AC:

5173

AN:

5188

South Asian (SAS)

AF:

0.903

AC:

4354

AN:

4822

European-Finnish (FIN)

AF:

0.920

AC:

9765

AN:

10614

Middle Eastern (MID)

AF:

0.973

AC:

286

AN:

294

European-Non Finnish (NFE)

AF:

0.902

AC:

61366

AN:

68026

Other (OTH)

AF:

0.955

AC:

2018

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

497

994

1491

1988

2485

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

910

1820

2730

3640

4550

<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:

0.916

Hom.:

77333

Bravo

AF:

0.939

Asia WGS

AF:

0.955

AC:

3321

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

2.1

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