Genetic Variant :null (chr3-172501054-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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 0.035 ( 19 hom., cov: 0)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.913

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=-1.06).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0906 is higher than 0.05.

Variant Effect in Transcripts

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0350

AC:

1816

AN:

51866

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0951

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0113

Gnomad ASJ

AF:

0.0405

Gnomad EAS

AF:

0.00233

Gnomad SAS

AF:

0.00528

Gnomad FIN

AF:

0.00450

Gnomad MID

AF:

0.0152

Gnomad NFE

AF:

0.0199

Gnomad OTH

AF:

0.0317

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

GnomAD4 genome

AF:

0.0350

AC:

1819

AN:

51940

Hom.:

Cov.:

AF XY:

0.0314

AC XY:

816

AN XY:

25962

show subpopulations

African (AFR)

AF:

0.0950

AC:

1241

AN:

13066

American (AMR)

AF:

0.0113

AC:

AN:

6286

Ashkenazi Jewish (ASJ)

AF:

0.0405

AC:

AN:

888

East Asian (EAS)

AF:

0.00234

AC:

AN:

3840

South Asian (SAS)

AF:

0.00528

AC:

AN:

2462

European-Finnish (FIN)

AF:

0.00450

AC:

AN:

3556

Middle Eastern (MID)

AF:

0.0156

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0199

AC:

413

AN:

20786

Other (OTH)

AF:

0.0304

AC:

AN:

626

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

177

265

354

442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

<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:

0.282

Hom.:

257

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.29

(source)

DANN

Benign

0.044

PhyloP100

-0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

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