Variant chr20-54174979-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 0.464 in 152,020 control chromosomes in the GnomAD database, including 17,317 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 0.46 ( 17317 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 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:

0.464

AC:

70423

AN:

151902

Hom.:

17272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.643

Gnomad AMI

AF:

0.417

Gnomad AMR

AF:

0.372

Gnomad ASJ

AF:

0.568

Gnomad EAS

AF:

0.372

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.355

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.397

Gnomad OTH

AF:

0.476

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

GnomAD4 genome

AF:

0.464

AC:

70521

AN:

152020

Hom.:

17317

Cov.:

AF XY:

0.460

AC XY:

34209

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.643

Gnomad4 AMR

AF:

0.371

Gnomad4 ASJ

AF:

0.568

Gnomad4 EAS

AF:

0.372

Gnomad4 SAS

AF:

0.413

Gnomad4 FIN

AF:

0.355

Gnomad4 NFE

AF:

0.397

Gnomad4 OTH

AF:

0.479

Alfa

AF:

0.415

Hom.:

29182

Bravo

AF:

0.471

Asia WGS

AF:

0.417

AC:

1447

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.9

DANN

Benign

0.76

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