Variant rs892034 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 0.636 in 152,118 control chromosomes in the GnomAD database, including 32,960 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 0.64 ( 32922 hom., cov: 30)

Exomes 𝑓: 0.55 ( 38 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.654

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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 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:

0.636

AC:

96529

AN:

151770

Hom.:

32858

Cov.:

show subpopulations

Gnomad AFR

AF:

0.886

Gnomad AMI

AF:

0.442

Gnomad AMR

AF:

0.611

Gnomad ASJ

AF:

0.569

Gnomad EAS

AF:

0.870

Gnomad SAS

AF:

0.573

Gnomad FIN

AF:

0.537

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.498

Gnomad OTH

AF:

0.614

GnomAD4 exome

AF:

0.548

AC:

126

AN:

230

Hom.:

Cov.:

AF XY:

0.560

AC XY:

AN XY:

168

show subpopulations

Gnomad4 AFR exome

AF:

0.750

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.455

Gnomad4 NFE exome

AF:

0.528

Gnomad4 OTH exome

AF:

0.688

GnomAD4 genome

AF:

0.636

AC:

96652

AN:

151888

Hom.:

32922

Cov.:

AF XY:

0.638

AC XY:

47383

AN XY:

74210

show subpopulations

Gnomad4 AFR

AF:

0.886

Gnomad4 AMR

AF:

0.611

Gnomad4 ASJ

AF:

0.569

Gnomad4 EAS

AF:

0.870

Gnomad4 SAS

AF:

0.572

Gnomad4 FIN

AF:

0.537

Gnomad4 NFE

AF:

0.498

Gnomad4 OTH

AF:

0.620

Alfa

AF:

0.529

Hom.:

23896

Bravo

AF:

0.658

Asia WGS

AF:

0.766

AC:

2663

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.7

DANN

Benign

0.73

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