Genetic Variant :null (chr2-184947213-A-C) – 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 0.349 in 147,360 control chromosomes in the GnomAD database, including 10,708 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 0.35 ( 10708 hom., cov: 26)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.30

Publications

25 publications found

Variant links:

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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 = 0.455 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:

0.349

AC:

51462

AN:

147282

Hom.:

10713

Cov.:

show subpopulations

Gnomad AFR

AF:

0.104

Gnomad AMI

AF:

0.437

Gnomad AMR

AF:

0.399

Gnomad ASJ

AF:

0.497

Gnomad EAS

AF:

0.434

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.383

Gnomad MID

AF:

0.336

Gnomad NFE

AF:

0.459

Gnomad OTH

AF:

0.370

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

GnomAD4 genome

AF:

0.349

AC:

51433

AN:

147360

Hom.:

10708

Cov.:

AF XY:

0.346

AC XY:

24742

AN XY:

71534

show subpopulations

African (AFR)

AF:

0.104

AC:

4133

AN:

39740

American (AMR)

AF:

0.398

AC:

5919

AN:

14870

Ashkenazi Jewish (ASJ)

AF:

0.497

AC:

1708

AN:

3440

East Asian (EAS)

AF:

0.433

AC:

2171

AN:

5014

South Asian (SAS)

AF:

0.402

AC:

1880

AN:

4680

European-Finnish (FIN)

AF:

0.383

AC:

3531

AN:

9216

Middle Eastern (MID)

AF:

0.332

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.459

AC:

30861

AN:

67192

Other (OTH)

AF:

0.366

AC:

741

AN:

2022

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

1404

2809

4213

5618

7022

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

504

1008

1512

2016

2520

<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:

0.447

Hom.:

19722

Bravo

AF:

0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.3

(source)

DANN

Benign

0.29

PhyloP100

1.3

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