Variant 19-3958399-A-G 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 0.792 in 456,038 control chromosomes in the GnomAD database, including 143,812 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 0.79 ( 47440 hom., cov: 34)

Exomes 𝑓: 0.79 ( 96372 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.10

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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:

0.787

AC:

119760

AN:

152100

Hom.:

47399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.749

Gnomad AMI

AF:

0.783

Gnomad AMR

AF:

0.856

Gnomad ASJ

AF:

0.721

Gnomad EAS

AF:

0.963

Gnomad SAS

AF:

0.771

Gnomad FIN

AF:

0.804

Gnomad MID

AF:

0.715

Gnomad NFE

AF:

0.785

Gnomad OTH

AF:

0.781

GnomAD4 exome

AF:

0.794

AC:

241171

AN:

303820

Hom.:

96372

AF XY:

0.791

AC XY:

136836

AN XY:

172998

show subpopulations

Gnomad4 AFR exome

AF:

0.742

Gnomad4 AMR exome

AF:

0.890

Gnomad4 ASJ exome

AF:

0.734

Gnomad4 EAS exome

AF:

0.966

Gnomad4 SAS exome

AF:

0.770

Gnomad4 FIN exome

AF:

0.789

Gnomad4 NFE exome

AF:

0.784

Gnomad4 OTH exome

AF:

0.793

GnomAD4 genome

AF:

0.787

AC:

119859

AN:

152218

Hom.:

47440

Cov.:

AF XY:

0.792

AC XY:

58935

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.749

Gnomad4 AMR

AF:

0.856

Gnomad4 ASJ

AF:

0.721

Gnomad4 EAS

AF:

0.963

Gnomad4 SAS

AF:

0.770

Gnomad4 FIN

AF:

0.804

Gnomad4 NFE

AF:

0.785

Gnomad4 OTH

AF:

0.782

Alfa

AF:

0.782

Hom.:

58217

Bravo

AF:

0.789

Asia WGS

AF:

0.865

AC:

3005

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.9

DANN

Benign

0.67

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