Variant rs1228439 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 152,042 control chromosomes in the GnomAD database, including 24,027 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 ( 24027 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.939

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 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:

0.556

AC:

84500

AN:

151924

Hom.:

24007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.471

Gnomad AMI

AF:

0.482

Gnomad AMR

AF:

0.614

Gnomad ASJ

AF:

0.488

Gnomad EAS

AF:

0.781

Gnomad SAS

AF:

0.449

Gnomad FIN

AF:

0.629

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.580

Gnomad OTH

AF:

0.537

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

GnomAD4 genome

AF:

0.556

AC:

84569

AN:

152042

Hom.:

24027

Cov.:

AF XY:

0.557

AC XY:

41361

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.471

Gnomad4 AMR

AF:

0.615

Gnomad4 ASJ

AF:

0.488

Gnomad4 EAS

AF:

0.782

Gnomad4 SAS

AF:

0.451

Gnomad4 FIN

AF:

0.629

Gnomad4 NFE

AF:

0.580

Gnomad4 OTH

AF:

0.533

Alfa

AF:

0.569

Hom.:

50267

Bravo

AF:

0.558

Asia WGS

AF:

0.563

AC:

1957

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.6

DANN

Benign

0.28

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