dbSNP rs2943634: :null (chr2-226203364-A-C) – 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 0.611 in 151,356 control chromosomes in the GnomAD database, including 29,487 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 0.61 ( 29487 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.790

Publications

126 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 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:

0.611

AC:

92411

AN:

151238

Hom.:

29465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.422

Gnomad AMI

AF:

0.631

Gnomad AMR

AF:

0.720

Gnomad ASJ

AF:

0.744

Gnomad EAS

AF:

0.909

Gnomad SAS

AF:

0.774

Gnomad FIN

AF:

0.645

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.655

Gnomad OTH

AF:

0.633

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

GnomAD4 genome

AF:

0.611

AC:

92466

AN:

151356

Hom.:

29487

Cov.:

AF XY:

0.614

AC XY:

45424

AN XY:

73944

show subpopulations

African (AFR)

AF:

0.421

AC:

17435

AN:

41376

American (AMR)

AF:

0.720

AC:

10918

AN:

15162

Ashkenazi Jewish (ASJ)

AF:

0.744

AC:

2569

AN:

3454

East Asian (EAS)

AF:

0.910

AC:

4664

AN:

5126

South Asian (SAS)

AF:

0.774

AC:

3731

AN:

4818

European-Finnish (FIN)

AF:

0.645

AC:

6800

AN:

10542

Middle Eastern (MID)

AF:

0.517

AC:

152

AN:

294

European-Non Finnish (NFE)

AF:

0.655

AC:

44285

AN:

67576

Other (OTH)

AF:

0.638

AC:

1338

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1733

3466

5198

6931

8664

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

766

1532

2298

3064

3830

<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:

0.655

Hom.:

127064

Bravo

AF:

0.612

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

5.0

(source)

DANN

Benign

0.75

PhyloP100

0.79

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