Genetic Variant :null (chr8-127486259-T-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 0.864 in 152,126 control chromosomes in the GnomAD database, including 57,023 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 0.86 ( 57023 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.68

Publications

5 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=-1.03).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.9 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:

0.865

AC:

131412

AN:

152008

Hom.:

56992

Cov.:

show subpopulations

Gnomad AFR

AF:

0.793

Gnomad AMI

AF:

0.904

Gnomad AMR

AF:

0.914

Gnomad ASJ

AF:

0.939

Gnomad EAS

AF:

0.843

Gnomad SAS

AF:

0.863

Gnomad FIN

AF:

0.836

Gnomad MID

AF:

0.940

Gnomad NFE

AF:

0.898

Gnomad OTH

AF:

0.884

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

GnomAD4 genome

AF:

0.864

AC:

131491

AN:

152126

Hom.:

57023

Cov.:

AF XY:

0.862

AC XY:

64092

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.793

AC:

32903

AN:

41500

American (AMR)

AF:

0.913

AC:

13966

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.939

AC:

3257

AN:

3470

East Asian (EAS)

AF:

0.843

AC:

4365

AN:

5176

South Asian (SAS)

AF:

0.864

AC:

4169

AN:

4826

European-Finnish (FIN)

AF:

0.836

AC:

8810

AN:

10534

Middle Eastern (MID)

AF:

0.949

AC:

279

AN:

294

European-Non Finnish (NFE)

AF:

0.898

AC:

61057

AN:

68004

Other (OTH)

AF:

0.879

AC:

1861

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

921

1841

2762

3682

4603

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

892

1784

2676

3568

4460

<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:

0.871

Hom.:

7202

Bravo

AF:

0.865

Asia WGS

AF:

0.803

AC:

2792

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.85

(source)

DANN

Benign

0.64

PhyloP100

-1.7

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