Variant rs6554759 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 0.853 in 152,324 control chromosomes in the GnomAD database, including 55,527 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 0.85 ( 55527 hom., cov: 35)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.02

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 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:

0.852

AC:

129747

AN:

152206

Hom.:

55472

Cov.:

show subpopulations

Gnomad AFR

AF:

0.898

Gnomad AMI

AF:

0.807

Gnomad AMR

AF:

0.875

Gnomad ASJ

AF:

0.781

Gnomad EAS

AF:

0.949

Gnomad SAS

AF:

0.916

Gnomad FIN

AF:

0.773

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.825

Gnomad OTH

AF:

0.846

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

GnomAD4 genome

AF:

0.853

AC:

129863

AN:

152324

Hom.:

55527

Cov.:

AF XY:

0.853

AC XY:

63509

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.898

Gnomad4 AMR

AF:

0.875

Gnomad4 ASJ

AF:

0.781

Gnomad4 EAS

AF:

0.949

Gnomad4 SAS

AF:

0.917

Gnomad4 FIN

AF:

0.773

Gnomad4 NFE

AF:

0.825

Gnomad4 OTH

AF:

0.846

Alfa

AF:

0.833

Hom.:

52260

Bravo

AF:

0.862

Asia WGS

AF:

0.927

AC:

3223

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.39

DANN

Benign

0.63

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