Variant rs790419 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 0.258 in 149,980 control chromosomes in the GnomAD database, including 5,182 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 0.26 ( 5182 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.14

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 (SAS) allele frequency at 95% confidence interval = 0.314 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:

0.258

AC:

38625

AN:

149866

Hom.:

5159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.314

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.326

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.227

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

GnomAD4 genome

AF:

0.258

AC:

38691

AN:

149980

Hom.:

5182

Cov.:

AF XY:

0.260

AC XY:

19025

AN XY:

73194

show subpopulations

Gnomad4 AFR

AF:

0.314

Gnomad4 AMR

AF:

0.275

Gnomad4 ASJ

AF:

0.248

Gnomad4 EAS

AF:

0.325

Gnomad4 SAS

AF:

0.328

Gnomad4 FIN

AF:

0.224

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.226

Alfa

AF:

0.123

Hom.:

202

Bravo

AF:

0.268

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.2

DANN

Benign

0.72

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