Genetic Variant :null (chr8-11486464-C-T) – 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 0.259 in 152,104 control chromosomes in the GnomAD database, including 6,491 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 0.26 ( 6491 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.878

Publications

204 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 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:

0.259

AC:

39383

AN:

151986

Hom.:

6471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.715

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.256

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

GnomAD4 genome

AF:

0.259

AC:

39418

AN:

152104

Hom.:

6491

Cov.:

AF XY:

0.267

AC XY:

19834

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.138

AC:

5734

AN:

41526

American (AMR)

AF:

0.444

AC:

6784

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

499

AN:

3470

East Asian (EAS)

AF:

0.716

AC:

3687

AN:

5152

South Asian (SAS)

AF:

0.350

AC:

1684

AN:

4812

European-Finnish (FIN)

AF:

0.274

AC:

2894

AN:

10568

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.255

AC:

17343

AN:

67974

Other (OTH)

AF:

0.266

AC:

562

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1410

2820

4230

5640

7050

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.265

Hom.:

27391

Bravo

AF:

0.274

Asia WGS

AF:

0.534

AC:

1855

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.1

(source)

DANN

Benign

0.72

PhyloP100

0.88

PromoterAI

-0.0080

Neutral

(source)

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