Variant rs6469488 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 0.912 in 152,256 control chromosomes in the GnomAD database, including 63,879 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 0.91 ( 63879 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602

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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.97 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:

0.912

AC:

138756

AN:

152138

Hom.:

63838

Cov.:

show subpopulations

Gnomad AFR

AF:

0.978

Gnomad AMI

AF:

0.879

Gnomad AMR

AF:

0.796

Gnomad ASJ

AF:

0.946

Gnomad EAS

AF:

0.599

Gnomad SAS

AF:

0.945

Gnomad FIN

AF:

0.883

Gnomad MID

AF:

0.981

Gnomad NFE

AF:

0.923

Gnomad OTH

AF:

0.901

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

GnomAD4 genome

AF:

0.912

AC:

138852

AN:

152256

Hom.:

63879

Cov.:

AF XY:

0.908

AC XY:

67577

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.978

Gnomad4 AMR

AF:

0.795

Gnomad4 ASJ

AF:

0.946

Gnomad4 EAS

AF:

0.598

Gnomad4 SAS

AF:

0.945

Gnomad4 FIN

AF:

0.883

Gnomad4 NFE

AF:

0.923

Gnomad4 OTH

AF:

0.901

Alfa

AF:

0.915

Hom.:

84094

Bravo

AF:

0.900

Asia WGS

AF:

0.794

AC:

2763

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.25

DANN

Benign

0.50

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