Variant chr20-6394813-T-A 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 0.294 in 152,080 control chromosomes in the GnomAD database, including 6,769 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 ( 6769 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.702

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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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:

0.294

AC:

44736

AN:

151962

Hom.:

6770

Cov.:

show subpopulations

Gnomad AFR

AF:

0.325

Gnomad AMI

AF:

0.223

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.247

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.320

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

GnomAD4 genome

AF:

0.294

AC:

44742

AN:

152080

Hom.:

6769

Cov.:

AF XY:

0.288

AC XY:

21369

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.324

Gnomad4 AMR

AF:

0.263

Gnomad4 ASJ

AF:

0.360

Gnomad4 EAS

AF:

0.110

Gnomad4 SAS

AF:

0.248

Gnomad4 FIN

AF:

0.248

Gnomad4 NFE

AF:

0.304

Gnomad4 OTH

AF:

0.317

Alfa

AF:

0.297

Hom.:

795

Bravo

AF:

0.294

Asia WGS

AF:

0.206

AC:

714

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.85

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