dbSNP rs6032664: :null (chr20-46110780-A-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 0.793 in 152,148 control chromosomes in the GnomAD database, including 48,547 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 0.79 ( 48547 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.164

Publications

24 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 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:

0.792

AC:

120463

AN:

152030

Hom.:

48473

Cov.:

show subpopulations

Gnomad AFR

AF:

0.939

Gnomad AMI

AF:

0.759

Gnomad AMR

AF:

0.775

Gnomad ASJ

AF:

0.731

Gnomad EAS

AF:

0.572

Gnomad SAS

AF:

0.738

Gnomad FIN

AF:

0.722

Gnomad MID

AF:

0.722

Gnomad NFE

AF:

0.743

Gnomad OTH

AF:

0.763

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

GnomAD4 genome

AF:

0.793

AC:

120598

AN:

152148

Hom.:

48547

Cov.:

AF XY:

0.787

AC XY:

58542

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.939

AC:

39028

AN:

41544

American (AMR)

AF:

0.776

AC:

11856

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.731

AC:

2534

AN:

3468

East Asian (EAS)

AF:

0.573

AC:

2962

AN:

5170

South Asian (SAS)

AF:

0.738

AC:

3556

AN:

4820

European-Finnish (FIN)

AF:

0.722

AC:

7616

AN:

10552

Middle Eastern (MID)

AF:

0.721

AC:

212

AN:

294

European-Non Finnish (NFE)

AF:

0.743

AC:

50523

AN:

67994

Other (OTH)

AF:

0.766

AC:

1620

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1223

2447

3670

4894

6117

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

868

1736

2604

3472

4340

<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:

0.781

Hom.:

5819

Bravo

AF:

0.803

Asia WGS

AF:

0.725

AC:

2522

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.4

(source)

DANN

Benign

0.83

PhyloP100

-0.16

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