dbSNP rs4298845: :null (chr10-83139600-G-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 0.791 in 152,120 control chromosomes in the GnomAD database, including 47,845 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 ( 47845 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Publications

2 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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.815 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:

0.791

AC:

120265

AN:

152002

Hom.:

47799

Cov.:

show subpopulations

Gnomad AFR

AF:

0.777

Gnomad AMI

AF:

0.903

Gnomad AMR

AF:

0.816

Gnomad ASJ

AF:

0.788

Gnomad EAS

AF:

0.541

Gnomad SAS

AF:

0.689

Gnomad FIN

AF:

0.780

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.821

Gnomad OTH

AF:

0.798

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

GnomAD4 genome

AF:

0.791

AC:

120366

AN:

152120

Hom.:

47845

Cov.:

AF XY:

0.788

AC XY:

58557

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.777

AC:

32258

AN:

41522

American (AMR)

AF:

0.816

AC:

12449

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.788

AC:

2736

AN:

3472

East Asian (EAS)

AF:

0.541

AC:

2795

AN:

5164

South Asian (SAS)

AF:

0.688

AC:

3318

AN:

4822

European-Finnish (FIN)

AF:

0.780

AC:

8248

AN:

10580

Middle Eastern (MID)

AF:

0.755

AC:

222

AN:

294

European-Non Finnish (NFE)

AF:

0.821

AC:

55830

AN:

67996

Other (OTH)

AF:

0.799

AC:

1688

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1300

2599

3899

5198

6498

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:

0.812

Hom.:

6254

Bravo

AF:

0.791

Asia WGS

AF:

0.665

AC:

2310

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.4

(source)

DANN

Benign

0.38

PhyloP100

-1.1

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