Variant rs522807 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 0.144 in 151,876 control chromosomes in the GnomAD database, including 3,591 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 0.14 ( 3591 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 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:

0.144

AC:

21822

AN:

151758

Hom.:

3585

Cov.:

show subpopulations

Gnomad AFR

AF:

0.409

Gnomad AMI

AF:

0.0451

Gnomad AMR

AF:

0.0668

Gnomad ASJ

AF:

0.0444

Gnomad EAS

AF:

0.0145

Gnomad SAS

AF:

0.0257

Gnomad FIN

AF:

0.0164

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0458

Gnomad OTH

AF:

0.123

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

GnomAD4 genome

AF:

0.144

AC:

21868

AN:

151876

Hom.:

3591

Cov.:

AF XY:

0.138

AC XY:

10248

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.409

Gnomad4 AMR

AF:

0.0667

Gnomad4 ASJ

AF:

0.0444

Gnomad4 EAS

AF:

0.0146

Gnomad4 SAS

AF:

0.0253

Gnomad4 FIN

AF:

0.0164

Gnomad4 NFE

AF:

0.0458

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.0624

Hom.:

1037

Bravo

AF:

0.159

Asia WGS

AF:

0.0500

AC:

174

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.019

DANN

Benign

0.54

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