Genetic Variant :null (chr4-4870520-A-G) – 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 0.645 in 152,132 control chromosomes in the GnomAD database, including 32,093 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 0.65 ( 32093 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.532

Publications

4 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 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:

0.645

AC:

98049

AN:

152014

Hom.:

32040

Cov.:

show subpopulations

Gnomad AFR

AF:

0.738

Gnomad AMI

AF:

0.454

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.678

Gnomad EAS

AF:

0.722

Gnomad SAS

AF:

0.562

Gnomad FIN

AF:

0.676

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.585

Gnomad OTH

AF:

0.618

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

GnomAD4 genome

AF:

0.645

AC:

98156

AN:

152132

Hom.:

32093

Cov.:

AF XY:

0.649

AC XY:

48260

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.738

AC:

30645

AN:

41512

American (AMR)

AF:

0.647

AC:

9896

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.678

AC:

2354

AN:

3470

East Asian (EAS)

AF:

0.721

AC:

3728

AN:

5168

South Asian (SAS)

AF:

0.562

AC:

2708

AN:

4818

European-Finnish (FIN)

AF:

0.676

AC:

7157

AN:

10590

Middle Eastern (MID)

AF:

0.636

AC:

187

AN:

294

European-Non Finnish (NFE)

AF:

0.585

AC:

39758

AN:

67976

Other (OTH)

AF:

0.621

AC:

1311

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1808

3616

5424

7232

9040

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

784

1568

2352

3136

3920

<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:

0.609

Hom.:

72957

Bravo

AF:

0.646

Asia WGS

AF:

0.615

AC:

2141

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.9

(source)

DANN

Benign

0.46

PhyloP100

-0.53

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