Genetic Variant :null (chr2-166680707-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.627 in 150,894 control chromosomes in the GnomAD database, including 31,639 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 0.63 ( 31639 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.610

Publications

1 publications found

Variant links:

Genome browser will be placed here

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 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:

0.628

AC:

94616

AN:

150780

Hom.:

31633

Cov.:

show subpopulations

Gnomad AFR

AF:

0.372

Gnomad AMI

AF:

0.729

Gnomad AMR

AF:

0.728

Gnomad ASJ

AF:

0.644

Gnomad EAS

AF:

0.572

Gnomad SAS

AF:

0.563

Gnomad FIN

AF:

0.728

Gnomad MID

AF:

0.667

Gnomad NFE

AF:

0.749

Gnomad OTH

AF:

0.641

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

GnomAD4 genome

AF:

0.627

AC:

94640

AN:

150894

Hom.:

31639

Cov.:

AF XY:

0.627

AC XY:

46167

AN XY:

73652

show subpopulations

African (AFR)

AF:

0.372

AC:

15263

AN:

41018

American (AMR)

AF:

0.728

AC:

11056

AN:

15196

Ashkenazi Jewish (ASJ)

AF:

0.644

AC:

2219

AN:

3448

East Asian (EAS)

AF:

0.572

AC:

2923

AN:

5114

South Asian (SAS)

AF:

0.564

AC:

2581

AN:

4578

European-Finnish (FIN)

AF:

0.728

AC:

7629

AN:

10476

Middle Eastern (MID)

AF:

0.666

AC:

193

AN:

290

European-Non Finnish (NFE)

AF:

0.749

AC:

50782

AN:

67774

Other (OTH)

AF:

0.637

AC:

1338

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1668

3336

5004

6672

8340

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

760

1520

2280

3040

3800

<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:

0.665

Hom.:

4548

Bravo

AF:

0.616

Asia WGS

AF:

0.546

AC:

1888

AN:

3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.36

(source)

DANN

Benign

0.52

PhyloP100

-0.61

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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