Variant rs6773018 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 0.465 in 152,142 control chromosomes in the GnomAD database, including 17,508 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 0.47 ( 17508 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.809

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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 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:

0.466

AC:

70769

AN:

152024

Hom.:

17493

Cov.:

show subpopulations

Gnomad AFR

AF:

0.602

Gnomad AMI

AF:

0.432

Gnomad AMR

AF:

0.361

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.0917

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.453

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.458

Gnomad OTH

AF:

0.419

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

GnomAD4 genome

AF:

0.465

AC:

70813

AN:

152142

Hom.:

17508

Cov.:

AF XY:

0.455

AC XY:

33804

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.602

Gnomad4 AMR

AF:

0.361

Gnomad4 ASJ

AF:

0.416

Gnomad4 EAS

AF:

0.0917

Gnomad4 SAS

AF:

0.238

Gnomad4 FIN

AF:

0.453

Gnomad4 NFE

AF:

0.458

Gnomad4 OTH

AF:

0.415

Alfa

AF:

0.462

Hom.:

2786

Bravo

AF:

0.468

Asia WGS

AF:

0.220

AC:

768

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.8

DANN

Benign

0.58

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