Variant chr20-6378394-A-G 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 0.289 in 152,132 control chromosomes in the GnomAD database, including 6,529 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 0.29 ( 6529 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178

Variant links:

Genome browser will be placed here

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 (NFE) allele frequency at 95% confidence interval = 0.309 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:

0.289

AC:

43900

AN:

152012

Hom.:

6531

Cov.:

show subpopulations

Gnomad AFR

AF:

0.284

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.113

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.319

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

GnomAD4 genome

AF:

0.289

AC:

43910

AN:

152132

Hom.:

6529

Cov.:

AF XY:

0.282

AC XY:

20948

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.284

Gnomad4 AMR

AF:

0.263

Gnomad4 ASJ

AF:

0.399

Gnomad4 EAS

AF:

0.113

Gnomad4 SAS

AF:

0.255

Gnomad4 FIN

AF:

0.246

Gnomad4 NFE

AF:

0.313

Gnomad4 OTH

AF:

0.316

Alfa

AF:

0.291

Hom.:

2060

Bravo

AF:

0.287

Asia WGS

AF:

0.209

AC:

726

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

1.3

DANN

Benign

0.61

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