dbSNP rs4392391: :null (chr3-44231474-G-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 0.477 in 152,040 control chromosomes in the GnomAD database, including 18,098 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 0.48 ( 18098 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252

Publications

3 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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:

0.477

AC:

72398

AN:

151920

Hom.:

18079

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.491

Gnomad AMR

AF:

0.542

Gnomad ASJ

AF:

0.529

Gnomad EAS

AF:

0.804

Gnomad SAS

AF:

0.702

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.474

Gnomad OTH

AF:

0.471

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

GnomAD4 genome

AF:

0.477

AC:

72462

AN:

152040

Hom.:

18098

Cov.:

AF XY:

0.484

AC XY:

36010

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.376

AC:

15587

AN:

41432

American (AMR)

AF:

0.543

AC:

8303

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.529

AC:

1836

AN:

3468

East Asian (EAS)

AF:

0.804

AC:

4171

AN:

5190

South Asian (SAS)

AF:

0.704

AC:

3395

AN:

4820

European-Finnish (FIN)

AF:

0.510

AC:

5382

AN:

10556

Middle Eastern (MID)

AF:

0.520

AC:

153

AN:

294

European-Non Finnish (NFE)

AF:

0.474

AC:

32198

AN:

67976

Other (OTH)

AF:

0.471

AC:

990

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1886

3773

5659

7546

9432

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

666

1332

1998

2664

3330

<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:

0.475

Hom.:

2938

Bravo

AF:

0.474

Asia WGS

AF:

0.726

AC:

2525

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.6

(source)

DANN

Benign

0.49

PhyloP100

0.25

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