dbSNP rs10489161: :null (chr1-25012308-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 0.325 in 152,086 control chromosomes in the GnomAD database, including 10,114 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 0.33 ( 10114 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.625

Publications

6 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 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:

0.325

AC:

49355

AN:

151968

Hom.:

10082

Cov.:

show subpopulations

Gnomad AFR

AF:

0.554

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.537

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.169

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.312

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

GnomAD4 genome

AF:

0.325

AC:

49441

AN:

152086

Hom.:

10114

Cov.:

AF XY:

0.325

AC XY:

24146

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.554

AC:

22982

AN:

41452

American (AMR)

AF:

0.338

AC:

5167

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

721

AN:

3472

East Asian (EAS)

AF:

0.536

AC:

2767

AN:

5158

South Asian (SAS)

AF:

0.416

AC:

2006

AN:

4818

European-Finnish (FIN)

AF:

0.169

AC:

1793

AN:

10598

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.195

AC:

13231

AN:

67980

Other (OTH)

AF:

0.317

AC:

668

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

1475

2950

4424

5899

7374

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<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:

0.244

Hom.:

17682

Bravo

AF:

0.350

Asia WGS

AF:

0.515

AC:

1790

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.9

(source)

DANN

Benign

0.41

PhyloP100

-0.63

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