Variant 1-53492930-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 0.443 in 152,184 control chromosomes in the GnomAD database, including 20,142 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 0.44 ( 20142 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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:

0.442

AC:

67278

AN:

152064

Hom.:

20087

Cov.:

show subpopulations

Gnomad AFR

AF:

0.857

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.266

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.423

Gnomad FIN

AF:

0.245

Gnomad MID

AF:

0.322

Gnomad NFE

AF:

0.270

Gnomad OTH

AF:

0.403

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

GnomAD4 genome

AF:

0.443

AC:

67391

AN:

152184

Hom.:

20142

Cov.:

AF XY:

0.438

AC XY:

32583

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.857

Gnomad4 AMR

AF:

0.275

Gnomad4 ASJ

AF:

0.266

Gnomad4 EAS

AF:

0.500

Gnomad4 SAS

AF:

0.424

Gnomad4 FIN

AF:

0.245

Gnomad4 NFE

AF:

0.270

Gnomad4 OTH

AF:

0.402

Alfa

AF:

0.307

Hom.:

4579

Bravo

AF:

0.460

Asia WGS

AF:

0.482

AC:

1678

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.20

DANN

Benign

0.55

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