dbSNP rs1894289: :null (chrX-23789751-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.393 in 110,359 control chromosomes in the GnomAD database, including 6,424 homozygotes. There are 12,419 hemizygotes in GnomAD. 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 0.39 ( 6424 hom., 12419 hem., cov: 22)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.17

Publications

1 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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

43384

AN:

110305

Hom.:

6425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.444

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.387

Gnomad SAS

AF:

0.306

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.390

Gnomad NFE

AF:

0.358

Gnomad OTH

AF:

0.406

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

GnomAD4 genome

AF:

0.393

AC:

43423

AN:

110359

Hom.:

6424

Cov.:

AF XY:

0.380

AC XY:

12419

AN XY:

32675

show subpopulations

African (AFR)

AF:

0.445

AC:

13494

AN:

30340

American (AMR)

AF:

0.490

AC:

5051

AN:

10303

Ashkenazi Jewish (ASJ)

AF:

0.349

AC:

921

AN:

2638

East Asian (EAS)

AF:

0.387

AC:

1348

AN:

3484

South Asian (SAS)

AF:

0.307

AC:

816

AN:

2656

European-Finnish (FIN)

AF:

0.345

AC:

1989

AN:

5758

Middle Eastern (MID)

AF:

0.381

AC:

AN:

215

European-Non Finnish (NFE)

AF:

0.358

AC:

18926

AN:

52799

Other (OTH)

AF:

0.405

AC:

608

AN:

1500

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

932

1864

2797

3729

4661

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

416

832

1248

1664

2080

<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:

0.378

Hom.:

31834

Bravo

AF:

0.413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

(source)

DANN

Benign

0.60

PhyloP100

1.2

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