Variant rs28386840 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 0.639 in 145,034 control chromosomes in the GnomAD database, including 29,748 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 0.64 ( 29748 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.104

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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 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:

0.639

AC:

92600

AN:

144926

Hom.:

29725

Cov.:

show subpopulations

Gnomad AFR

AF:

0.455

Gnomad AMI

AF:

0.662

Gnomad AMR

AF:

0.694

Gnomad ASJ

AF:

0.668

Gnomad EAS

AF:

0.559

Gnomad SAS

AF:

0.712

Gnomad FIN

AF:

0.735

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.709

Gnomad OTH

AF:

0.640

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

GnomAD4 genome

AF:

0.639

AC:

92666

AN:

145034

Hom.:

29748

Cov.:

AF XY:

0.644

AC XY:

45735

AN XY:

70978

show subpopulations

Gnomad4 AFR

AF:

0.455

Gnomad4 AMR

AF:

0.694

Gnomad4 ASJ

AF:

0.668

Gnomad4 EAS

AF:

0.559

Gnomad4 SAS

AF:

0.712

Gnomad4 FIN

AF:

0.735

Gnomad4 NFE

AF:

0.709

Gnomad4 OTH

AF:

0.644

Alfa

AF:

0.367

Hom.:

530

Bravo

AF:

0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.6

DANN

Benign

0.57

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