Variant rs5861423 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.57 ( 24189 hom., cov: 0)

Exomes 𝑓: 0.57 ( 77399 hom. )

Consequence

Unknown

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.155

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 4-119322234-A-ACTACT is Benign according to our data. Variant chr4-119322234-A-ACTACT is described in ClinVar as [Benign]. Clinvar id is 1261472.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.565

AC:

85520

AN:

151306

Hom.:

24156

Cov.:

show subpopulations

Gnomad AFR

AF:

0.556

Gnomad AMI

AF:

0.445

Gnomad AMR

AF:

0.603

Gnomad ASJ

AF:

0.621

Gnomad EAS

AF:

0.627

Gnomad SAS

AF:

0.533

Gnomad FIN

AF:

0.509

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.567

Gnomad OTH

AF:

0.595

GnomAD4 exome

AF:

0.569

AC:

266077

AN:

468010

Hom.:

77399

Cov.:

AF XY:

0.566

AC XY:

141477

AN XY:

250084

show subpopulations

Gnomad4 AFR exome

AF:

0.570

Gnomad4 AMR exome

AF:

0.654

Gnomad4 ASJ exome

AF:

0.638

Gnomad4 EAS exome

AF:

0.572

Gnomad4 SAS exome

AF:

0.541

Gnomad4 FIN exome

AF:

0.508

Gnomad4 NFE exome

AF:

0.569

Gnomad4 OTH exome

AF:

0.585

GnomAD4 genome

AF:

0.565

AC:

85618

AN:

151424

Hom.:

24189

Cov.:

AF XY:

0.562

AC XY:

41569

AN XY:

73946

show subpopulations

Gnomad4 AFR

AF:

0.556

Gnomad4 AMR

AF:

0.604

Gnomad4 ASJ

AF:

0.621

Gnomad4 EAS

AF:

0.627

Gnomad4 SAS

AF:

0.533

Gnomad4 FIN

AF:

0.509

Gnomad4 NFE

AF:

0.567

Gnomad4 OTH

AF:

0.599

Alfa

AF:

0.357

Hom.:

629

Asia WGS

AF:

0.633

AC:

2203

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over