Variant rs4390300 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 0.556 in 152,054 control chromosomes in the GnomAD database, including 25,194 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 0.56 ( 25194 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0790

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 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:

0.556

AC:

84448

AN:

151936

Hom.:

25161

Cov.:

show subpopulations

Gnomad AFR

AF:

0.791

Gnomad AMI

AF:

0.587

Gnomad AMR

AF:

0.476

Gnomad ASJ

AF:

0.553

Gnomad EAS

AF:

0.489

Gnomad SAS

AF:

0.432

Gnomad FIN

AF:

0.382

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.472

Gnomad OTH

AF:

0.550

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

GnomAD4 genome

AF:

0.556

AC:

84531

AN:

152054

Hom.:

25194

Cov.:

AF XY:

0.547

AC XY:

40654

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.791

Gnomad4 AMR

AF:

0.475

Gnomad4 ASJ

AF:

0.553

Gnomad4 EAS

AF:

0.489

Gnomad4 SAS

AF:

0.430

Gnomad4 FIN

AF:

0.382

Gnomad4 NFE

AF:

0.472

Gnomad4 OTH

AF:

0.546

Alfa

AF:

0.509

Hom.:

4945

Bravo

AF:

0.575

Asia WGS

AF:

0.439

AC:

1527

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.4

DANN

Benign

0.51

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