Variant chr19-39773326-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 0.712 in 151,774 control chromosomes in the GnomAD database, including 39,676 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 0.71 ( 39676 hom., cov: 29)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 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:

0.712

AC:

107980

AN:

151652

Hom.:

39607

Cov.:

show subpopulations

Gnomad AFR

AF:

0.893

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.703

Gnomad ASJ

AF:

0.683

Gnomad EAS

AF:

0.529

Gnomad SAS

AF:

0.577

Gnomad FIN

AF:

0.685

Gnomad MID

AF:

0.596

Gnomad NFE

AF:

0.636

Gnomad OTH

AF:

0.702

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

GnomAD4 genome

AF:

0.712

AC:

108105

AN:

151774

Hom.:

39676

Cov.:

AF XY:

0.713

AC XY:

52872

AN XY:

74164

show subpopulations

Gnomad4 AFR

AF:

0.894

Gnomad4 AMR

AF:

0.704

Gnomad4 ASJ

AF:

0.683

Gnomad4 EAS

AF:

0.529

Gnomad4 SAS

AF:

0.575

Gnomad4 FIN

AF:

0.685

Gnomad4 NFE

AF:

0.636

Gnomad4 OTH

AF:

0.703

Alfa

AF:

0.652

Hom.:

46218

Bravo

AF:

0.720

Asia WGS

AF:

0.602

AC:

2095

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.3

DANN

Benign

0.58

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