Variant rs1800776 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.0573 in 482,760 control chromosomes in the GnomAD database, including 1,005 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 0.055 ( 274 hom., cov: 33)

Exomes 𝑓: 0.059 ( 731 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.620

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0547

AC:

8313

AN:

152090

Hom.:

273

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0324

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.0551

Gnomad ASJ

AF:

0.0611

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0315

Gnomad FIN

AF:

0.0301

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.0754

Gnomad OTH

AF:

0.0646

GnomAD3 exomes

AF:

0.0520

AC:

9140

AN:

175874

Hom.:

299

AF XY:

0.0526

AC XY:

5058

AN XY:

96146

show subpopulations

Gnomad AFR exome

AF:

0.0287

Gnomad AMR exome

AF:

0.0463

Gnomad ASJ exome

AF:

0.0588

Gnomad EAS exome

AF:

0.000414

Gnomad SAS exome

AF:

0.0335

Gnomad FIN exome

AF:

0.0294

Gnomad NFE exome

AF:

0.0735

Gnomad OTH exome

AF:

0.0724

GnomAD4 exome

AF:

0.0586

AC:

19365

AN:

330552

Hom.:

731

Cov.:

AF XY:

0.0575

AC XY:

10853

AN XY:

188680

show subpopulations

Gnomad4 AFR exome

AF:

0.0303

Gnomad4 AMR exome

AF:

0.0474

Gnomad4 ASJ exome

AF:

0.0608

Gnomad4 EAS exome

AF:

0.000337

Gnomad4 SAS exome

AF:

0.0329

Gnomad4 FIN exome

AF:

0.0327

Gnomad4 NFE exome

AF:

0.0757

Gnomad4 OTH exome

AF:

0.0673

GnomAD4 genome

AF:

0.0546

AC:

8313

AN:

152208

Hom.:

274

Cov.:

AF XY:

0.0519

AC XY:

3865

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0323

Gnomad4 AMR

AF:

0.0549

Gnomad4 ASJ

AF:

0.0611

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0316

Gnomad4 FIN

AF:

0.0301

Gnomad4 NFE

AF:

0.0754

Gnomad4 OTH

AF:

0.0634

Alfa

AF:

0.0619

Hom.:

Bravo

AF:

0.0571

Asia WGS

AF:

0.0190

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.2

DANN

Benign

0.71

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over