Genetic Variant :null (chr8-58508057-G-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 0.671 in 151,958 control chromosomes in the GnomAD database, including 34,950 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 0.67 ( 34950 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.496

Publications

5 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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:

0.671

AC:

101902

AN:

151840

Hom.:

34908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.819

Gnomad AMI

AF:

0.568

Gnomad AMR

AF:

0.727

Gnomad ASJ

AF:

0.624

Gnomad EAS

AF:

0.632

Gnomad SAS

AF:

0.603

Gnomad FIN

AF:

0.564

Gnomad MID

AF:

0.624

Gnomad NFE

AF:

0.597

Gnomad OTH

AF:

0.662

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

GnomAD4 genome

AF:

0.671

AC:

102000

AN:

151958

Hom.:

34950

Cov.:

AF XY:

0.669

AC XY:

49673

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.819

AC:

33961

AN:

41448

American (AMR)

AF:

0.727

AC:

11107

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.624

AC:

2165

AN:

3470

East Asian (EAS)

AF:

0.633

AC:

3267

AN:

5162

South Asian (SAS)

AF:

0.602

AC:

2895

AN:

4810

European-Finnish (FIN)

AF:

0.564

AC:

5947

AN:

10538

Middle Eastern (MID)

AF:

0.640

AC:

187

AN:

292

European-Non Finnish (NFE)

AF:

0.597

AC:

40564

AN:

67950

Other (OTH)

AF:

0.659

AC:

1390

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1641

3282

4924

6565

8206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

800

1600

2400

3200

4000

<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:

0.468

Hom.:

1104

Bravo

AF:

0.691

Asia WGS

AF:

0.625

AC:

2173

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

5.8

(source)

DANN

Benign

0.74

PhyloP100

-0.50

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