dbSNP rs10484429: :null (chr6-48883913-C-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 0.101 in 151,998 control chromosomes in the GnomAD database, including 877 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 0.10 ( 877 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0680

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 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:

0.101

AC:

15270

AN:

151880

Hom.:

875

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.0493

Gnomad AMR

AF:

0.0705

Gnomad ASJ

AF:

0.0462

Gnomad EAS

AF:

0.0850

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.0836

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0709

Gnomad OTH

AF:

0.106

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

GnomAD4 genome

AF:

0.101

AC:

15280

AN:

151998

Hom.:

877

Cov.:

AF XY:

0.102

AC XY:

7573

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.164

AC:

6823

AN:

41490

American (AMR)

AF:

0.0704

AC:

1072

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.0462

AC:

160

AN:

3464

East Asian (EAS)

AF:

0.0850

AC:

439

AN:

5166

South Asian (SAS)

AF:

0.162

AC:

777

AN:

4808

European-Finnish (FIN)

AF:

0.0836

AC:

885

AN:

10592

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0710

AC:

4821

AN:

67932

Other (OTH)

AF:

0.105

AC:

222

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

679

1358

2036

2715

3394

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.0801

Hom.:

2328

Bravo

AF:

0.102

Asia WGS

AF:

0.110

AC:

382

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

5.9

(source)

DANN

Benign

0.45

PhyloP100

0.068

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