Variant rs1085832 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 0.801 in 152,206 control chromosomes in the GnomAD database, including 49,233 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 0.80 ( 49220 hom., cov: 32)

Exomes 𝑓: 0.82 ( 13 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.00

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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 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:

0.801

AC:

121765

AN:

152048

Hom.:

49184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.895

Gnomad AMI

AF:

0.704

Gnomad AMR

AF:

0.813

Gnomad ASJ

AF:

0.732

Gnomad EAS

AF:

0.900

Gnomad SAS

AF:

0.754

Gnomad FIN

AF:

0.773

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.747

Gnomad OTH

AF:

0.788

GnomAD4 exome

AF:

0.825

AC:

AN:

Hom.:

AF XY:

0.813

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 AMR exome

AF:

1.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.750

Gnomad4 NFE exome

AF:

0.821

GnomAD4 genome

AF:

0.801

AC:

121846

AN:

152166

Hom.:

49220

Cov.:

AF XY:

0.803

AC XY:

59700

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.895

Gnomad4 AMR

AF:

0.812

Gnomad4 ASJ

AF:

0.732

Gnomad4 EAS

AF:

0.900

Gnomad4 SAS

AF:

0.753

Gnomad4 FIN

AF:

0.773

Gnomad4 NFE

AF:

0.747

Gnomad4 OTH

AF:

0.778

Alfa

AF:

0.770

Hom.:

5612

Bravo

AF:

0.810

Asia WGS

AF:

0.787

AC:

2736

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.1

DANN

Benign

0.34

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