Variant 1-20588679-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 0.246 in 152,214 control chromosomes in the GnomAD database, including 5,647 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 0.25 ( 5647 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.295

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 (NFE) allele frequency at 95% confidence interval = 0.326 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:

0.246

AC:

37376

AN:

152096

Hom.:

5646

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0854

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.410

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.212

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.286

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

GnomAD4 genome

AF:

0.246

AC:

37379

AN:

152214

Hom.:

5647

Cov.:

AF XY:

0.242

AC XY:

17976

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.0852

Gnomad4 AMR

AF:

0.325

Gnomad4 ASJ

AF:

0.410

Gnomad4 EAS

AF:

0.133

Gnomad4 SAS

AF:

0.216

Gnomad4 FIN

AF:

0.212

Gnomad4 NFE

AF:

0.330

Gnomad4 OTH

AF:

0.282

Alfa

AF:

0.322

Hom.:

9050

Bravo

AF:

0.247

Asia WGS

AF:

0.187

AC:

649

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

9.9

DANN

Benign

0.67

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