Genetic Variant :null (chrX-67210798-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.65 ( 20380 hom., 21350 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.994

Variant links:

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ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.652

AC:

71694

AN:

109901

Hom.:

20390

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.890

Gnomad AMR

AF:

0.828

Gnomad ASJ

AF:

0.919

Gnomad EAS

AF:

0.998

Gnomad SAS

AF:

0.917

Gnomad FIN

AF:

0.829

Gnomad MID

AF:

0.760

Gnomad NFE

AF:

0.843

Gnomad OTH

AF:

0.695

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.652

AC:

71680

AN:

109954

Hom.:

20380

Cov.:

AF XY:

0.662

AC XY:

21350

AN XY:

32236

show subpopulations

African (AFR)

AF:

0.138

AC:

4191

AN:

30445

American (AMR)

AF:

0.828

AC:

8441

AN:

10195

Ashkenazi Jewish (ASJ)

AF:

0.919

AC:

2413

AN:

2627

East Asian (EAS)

AF:

0.998

AC:

3465

AN:

3471

South Asian (SAS)

AF:

0.917

AC:

2336

AN:

2548

European-Finnish (FIN)

AF:

0.829

AC:

4686

AN:

5656

Middle Eastern (MID)

AF:

0.756

AC:

161

AN:

213

European-Non Finnish (NFE)

AF:

0.843

AC:

44356

AN:

52646

Other (OTH)

AF:

0.697

AC:

1031

AN:

1479

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

482

963

1445

1926

2408

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.814

Hom.:

23663

Bravo

AF:

0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

7.1

(source)

DANN

Benign

0.61

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

chrX-67210798-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over