Variant rs790146 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 0.284 in 140,632 control chromosomes in the GnomAD database, including 6,203 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 0.28 ( 6203 hom., cov: 21)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.703

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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:

0.284

AC:

39960

AN:

140570

Hom.:

6195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.303

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.287

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

GnomAD4 genome

AF:

0.284

AC:

39978

AN:

140632

Hom.:

6203

Cov.:

AF XY:

0.280

AC XY:

18977

AN XY:

67784

show subpopulations

Gnomad4 AFR

AF:

0.183

Gnomad4 AMR

AF:

0.408

Gnomad4 ASJ

AF:

0.348

Gnomad4 EAS

AF:

0.451

Gnomad4 SAS

AF:

0.221

Gnomad4 FIN

AF:

0.214

Gnomad4 NFE

AF:

0.311

Gnomad4 OTH

AF:

0.287

Alfa

AF:

0.280

Hom.:

825

Bravo

AF:

0.294

Asia WGS

AF:

0.298

AC:

1036

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

4.1

DANN

Benign

0.65

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