Variant 20-6780865-C-T 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 0.703 in 152,048 control chromosomes in the GnomAD database, including 38,735 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 0.70 ( 38735 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.206

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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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:

0.703

AC:

106759

AN:

151928

Hom.:

38690

Cov.:

show subpopulations

Gnomad AFR

AF:

0.886

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.683

Gnomad ASJ

AF:

0.821

Gnomad EAS

AF:

0.672

Gnomad SAS

AF:

0.569

Gnomad FIN

AF:

0.574

Gnomad MID

AF:

0.756

Gnomad NFE

AF:

0.622

Gnomad OTH

AF:

0.715

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

GnomAD4 genome

AF:

0.703

AC:

106849

AN:

152048

Hom.:

38735

Cov.:

AF XY:

0.696

AC XY:

51754

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.886

Gnomad4 AMR

AF:

0.683

Gnomad4 ASJ

AF:

0.821

Gnomad4 EAS

AF:

0.672

Gnomad4 SAS

AF:

0.568

Gnomad4 FIN

AF:

0.574

Gnomad4 NFE

AF:

0.622

Gnomad4 OTH

AF:

0.708

Alfa

AF:

0.698

Hom.:

6422

Bravo

AF:

0.723

Asia WGS

AF:

0.609

AC:

2114

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

9.4

DANN

Benign

0.66

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