dbSNP rs10999530: :null (chr10-70767697-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The variant allele was found at a frequency of 0.0278 in 135,778 control chromosomes in the GnomAD database, including 41 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 0.028 ( 41 hom., cov: 26)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.507

Publications

4 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=-0.83).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0278 (3780/135778) while in subpopulation NFE AF = 0.0416 (2450/58942). AF 95% confidence interval is 0.0402. There are 41 homozygotes in GnomAd4. There are 1771 alleles in the male GnomAd4 subpopulation. Median coverage is 26. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 41 gene

Variant Effect in Transcripts

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0279

AC:

3785

AN:

135640

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00639

Gnomad AMI

AF:

0.0798

Gnomad AMR

AF:

0.0195

Gnomad ASJ

AF:

0.0355

Gnomad EAS

AF:

0.0321

Gnomad SAS

AF:

0.0262

Gnomad FIN

AF:

0.0390

Gnomad MID

AF:

0.0278

Gnomad NFE

AF:

0.0416

Gnomad OTH

AF:

0.0276

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

GnomAD4 genome

AF:

0.0278

AC:

3780

AN:

135778

Hom.:

Cov.:

AF XY:

0.0268

AC XY:

1771

AN XY:

66078

show subpopulations

African (AFR)

AF:

0.00637

AC:

254

AN:

39872

American (AMR)

AF:

0.0195

AC:

273

AN:

14004

Ashkenazi Jewish (ASJ)

AF:

0.0355

AC:

110

AN:

3098

East Asian (EAS)

AF:

0.0319

AC:

139

AN:

4356

South Asian (SAS)

AF:

0.0262

AC:

110

AN:

4204

European-Finnish (FIN)

AF:

0.0390

AC:

331

AN:

8490

Middle Eastern (MID)

AF:

0.0216

AC:

AN:

232

European-Non Finnish (NFE)

AF:

0.0416

AC:

2450

AN:

58942

Other (OTH)

AF:

0.0273

AC:

AN:

1866

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

144

288

433

577

721

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0792

Hom.:

Bravo

AF:

0.0696

Asia WGS

AF:

0.0340

AC:

114

AN:

3340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.3

(source)

DANN

Benign

0.87

PhyloP100

0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

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