Variant 19-54713574-A-C 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 0.745 in 158,124 control chromosomes in the GnomAD database, including 44,509 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 0.75 ( 42953 hom., cov: 31)

Exomes 𝑓: 0.71 ( 1556 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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:

0.746

AC:

113354

AN:

151900

Hom.:

42902

Cov.:

show subpopulations

Gnomad AFR

AF:

0.844

Gnomad AMI

AF:

0.642

Gnomad AMR

AF:

0.781

Gnomad ASJ

AF:

0.576

Gnomad EAS

AF:

0.986

Gnomad SAS

AF:

0.756

Gnomad FIN

AF:

0.704

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.678

Gnomad OTH

AF:

0.725

GnomAD4 exome

AF:

0.709

AC:

4331

AN:

6106

Hom.:

1556

AF XY:

0.720

AC XY:

2279

AN XY:

3166

show subpopulations

Gnomad4 AFR exome

AF:

0.841

Gnomad4 AMR exome

AF:

0.818

Gnomad4 ASJ exome

AF:

0.689

Gnomad4 EAS exome

AF:

0.983

Gnomad4 SAS exome

AF:

0.735

Gnomad4 FIN exome

AF:

0.674

Gnomad4 NFE exome

AF:

0.685

Gnomad4 OTH exome

AF:

0.686

GnomAD4 genome

AF:

0.746

AC:

113466

AN:

152018

Hom.:

42953

Cov.:

AF XY:

0.748

AC XY:

55570

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.844

Gnomad4 AMR

AF:

0.781

Gnomad4 ASJ

AF:

0.576

Gnomad4 EAS

AF:

0.986

Gnomad4 SAS

AF:

0.756

Gnomad4 FIN

AF:

0.704

Gnomad4 NFE

AF:

0.678

Gnomad4 OTH

AF:

0.726

Alfa

AF:

0.687

Hom.:

41066

Bravo

AF:

0.757

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

3.0

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