Genetic Variant :null (chr20-6780865-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 0.703 in 152,048 control chromosomes in the GnomAD database, including 38,735 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 0.70 ( 38735 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.206

Publications

10 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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:

0.703

AC:

106759

AN:

151928

Hom.:

38690

Cov.:

show subpopulations

Gnomad AFR

AF:

0.886

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.683

Gnomad ASJ

AF:

0.821

Gnomad EAS

AF:

0.672

Gnomad SAS

AF:

0.569

Gnomad FIN

AF:

0.574

Gnomad MID

AF:

0.756

Gnomad NFE

AF:

0.622

Gnomad OTH

AF:

0.715

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

GnomAD4 genome

AF:

0.703

AC:

106849

AN:

152048

Hom.:

38735

Cov.:

AF XY:

0.696

AC XY:

51754

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.886

AC:

36779

AN:

41520

American (AMR)

AF:

0.683

AC:

10439

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.821

AC:

2847

AN:

3468

East Asian (EAS)

AF:

0.672

AC:

3465

AN:

5156

South Asian (SAS)

AF:

0.568

AC:

2728

AN:

4806

European-Finnish (FIN)

AF:

0.574

AC:

6046

AN:

10542

Middle Eastern (MID)

AF:

0.752

AC:

221

AN:

294

European-Non Finnish (NFE)

AF:

0.622

AC:

42262

AN:

67958

Other (OTH)

AF:

0.708

AC:

1489

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1524

3048

4571

6095

7619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

810

1620

2430

3240

4050

<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:

0.687

Hom.:

12379

Bravo

AF:

0.723

Asia WGS

AF:

0.609

AC:

2114

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

9.4

(source)

DANN

Benign

0.66

PhyloP100

-0.21

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