Genetic Variant :null (chr5-108580035-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 0.688 in 152,076 control chromosomes in the GnomAD database, including 37,381 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 0.69 ( 37381 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.535

Publications

14 publications found

Variant links:

COSMIC-nc: COSV60180725

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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:

0.688

AC:

104563

AN:

151956

Hom.:

37326

Cov.:

show subpopulations

Gnomad AFR

AF:

0.860

Gnomad AMI

AF:

0.746

Gnomad AMR

AF:

0.616

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.316

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.644

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.656

Gnomad OTH

AF:

0.671

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

GnomAD4 genome

AF:

0.688

AC:

104669

AN:

152076

Hom.:

37381

Cov.:

AF XY:

0.680

AC XY:

50533

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.860

AC:

35713

AN:

41506

American (AMR)

AF:

0.615

AC:

9412

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.669

AC:

2321

AN:

3470

East Asian (EAS)

AF:

0.315

AC:

1623

AN:

5146

South Asian (SAS)

AF:

0.400

AC:

1925

AN:

4808

European-Finnish (FIN)

AF:

0.644

AC:

6798

AN:

10558

Middle Eastern (MID)

AF:

0.646

AC:

190

AN:

294

European-Non Finnish (NFE)

AF:

0.656

AC:

44599

AN:

67980

Other (OTH)

AF:

0.668

AC:

1409

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1547

3094

4640

6187

7734

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<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:

0.661

Hom.:

133255

Bravo

AF:

0.694

Asia WGS

AF:

0.420

AC:

1464

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.1

(source)

DANN

Benign

0.84

PhyloP100

-0.54

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