dbSNP rs10485662: :null (chr20-39846564-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 0.175 in 152,104 control chromosomes in the GnomAD database, including 2,412 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 0.17 ( 2412 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.447

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 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:

0.175

AC:

26565

AN:

151986

Hom.:

2409

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.147

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.282

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.169

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

GnomAD4 genome

AF:

0.175

AC:

26587

AN:

152104

Hom.:

2412

Cov.:

AF XY:

0.176

AC XY:

13114

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.138

AC:

5743

AN:

41500

American (AMR)

AF:

0.148

AC:

2255

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

535

AN:

3464

East Asian (EAS)

AF:

0.282

AC:

1455

AN:

5162

South Asian (SAS)

AF:

0.262

AC:

1260

AN:

4818

European-Finnish (FIN)

AF:

0.170

AC:

1796

AN:

10590

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.190

AC:

12912

AN:

67980

Other (OTH)

AF:

0.175

AC:

369

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1126

2253

3379

4506

5632

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

314

628

942

1256

1570

<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:

0.184

Hom.:

4436

Bravo

AF:

0.169

Asia WGS

AF:

0.294

AC:

1019

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.0

(source)

DANN

Benign

0.70

PhyloP100

-0.45

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