Variant chr1-53890688-C-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 0.159 in 452,482 control chromosomes in the GnomAD database, including 6,483 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 0.13 ( 1471 hom., cov: 32)

Exomes 𝑓: 0.17 ( 5012 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.43

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 (SAS) allele frequency at 95% confidence interval = 0.236 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:

0.131

AC:

19947

AN:

152058

Hom.:

1472

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0668

Gnomad AMI

AF:

0.0779

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.183

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.249

Gnomad FIN

AF:

0.0985

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.146

GnomAD4 exome

AF:

0.174

AC:

52192

AN:

300306

Hom.:

5012

AF XY:

0.179

AC XY:

30521

AN XY:

170718

show subpopulations

Gnomad4 AFR exome

AF:

0.0671

Gnomad4 AMR exome

AF:

0.222

Gnomad4 ASJ exome

AF:

0.183

Gnomad4 EAS exome

AF:

0.172

Gnomad4 SAS exome

AF:

0.238

Gnomad4 FIN exome

AF:

0.110

Gnomad4 NFE exome

AF:

0.152

Gnomad4 OTH exome

AF:

0.157

GnomAD4 genome

AF:

0.131

AC:

19930

AN:

152176

Hom.:

1471

Cov.:

AF XY:

0.132

AC XY:

9813

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0666

Gnomad4 AMR

AF:

0.177

Gnomad4 ASJ

AF:

0.183

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.248

Gnomad4 FIN

AF:

0.0985

Gnomad4 NFE

AF:

0.151

Gnomad4 OTH

AF:

0.144

Alfa

AF:

0.141

Hom.:

269

Bravo

AF:

0.132

Asia WGS

AF:

0.216

AC:

752

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

8.7

DANN

Benign

0.62

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