dbSNP rs4392363: :null (chr3-67093414-T-A) – 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 0.322 in 152,044 control chromosomes in the GnomAD database, including 8,593 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 0.32 ( 8593 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.932

Publications

8 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 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:

0.322

AC:

48852

AN:

151926

Hom.:

8580

Cov.:

show subpopulations

Gnomad AFR

AF:

0.464

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.280

Gnomad ASJ

AF:

0.237

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.338

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.314

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

GnomAD4 genome

AF:

0.322

AC:

48897

AN:

152044

Hom.:

8593

Cov.:

AF XY:

0.316

AC XY:

23515

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.465

AC:

19259

AN:

41452

American (AMR)

AF:

0.279

AC:

4256

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.237

AC:

823

AN:

3468

East Asian (EAS)

AF:

0.449

AC:

2325

AN:

5176

South Asian (SAS)

AF:

0.337

AC:

1626

AN:

4820

European-Finnish (FIN)

AF:

0.173

AC:

1828

AN:

10590

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.262

AC:

17825

AN:

67968

Other (OTH)

AF:

0.313

AC:

662

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1659

3318

4978

6637

8296

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

476

952

1428

1904

2380

<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:

0.290

Hom.:

949

Bravo

AF:

0.337

Asia WGS

AF:

0.370

AC:

1283

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.29

(source)

DANN

Benign

0.29

PhyloP100

-0.93

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