Variant 20-22234183-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 0.336 in 152,168 control chromosomes in the GnomAD database, including 9,178 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 0.34 ( 9178 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.27

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=-0.63).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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:

0.336

AC:

51150

AN:

152050

Hom.:

9176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.414

Gnomad EAS

AF:

0.684

Gnomad SAS

AF:

0.373

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.354

Gnomad OTH

AF:

0.373

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

GnomAD4 genome

AF:

0.336

AC:

51172

AN:

152168

Hom.:

9178

Cov.:

AF XY:

0.336

AC XY:

24978

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.245

Gnomad4 AMR

AF:

0.396

Gnomad4 ASJ

AF:

0.414

Gnomad4 EAS

AF:

0.684

Gnomad4 SAS

AF:

0.373

Gnomad4 FIN

AF:

0.274

Gnomad4 NFE

AF:

0.354

Gnomad4 OTH

AF:

0.375

Alfa

AF:

0.354

Hom.:

7054

Bravo

AF:

0.343

Asia WGS

AF:

0.476

AC:

1655

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

DANN

Benign

0.65

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