Variant rs6763848 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 0.31 in 152,088 control chromosomes in the GnomAD database, including 7,919 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 0.31 ( 7919 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0340

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 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:

0.310

AC:

47175

AN:

151970

Hom.:

7919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.237

Gnomad AMR

AF:

0.343

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.668

Gnomad SAS

AF:

0.525

Gnomad FIN

AF:

0.285

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.314

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

GnomAD4 genome

AF:

0.310

AC:

47189

AN:

152088

Hom.:

7919

Cov.:

AF XY:

0.315

AC XY:

23449

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.245

Gnomad4 AMR

AF:

0.343

Gnomad4 ASJ

AF:

0.222

Gnomad4 EAS

AF:

0.668

Gnomad4 SAS

AF:

0.524

Gnomad4 FIN

AF:

0.285

Gnomad4 NFE

AF:

0.310

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.299

Hom.:

7207

Bravo

AF:

0.306

Asia WGS

AF:

0.575

AC:

1998

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.9

DANN

Benign

0.17

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