Variant rs1328244 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 0.855 in 152,228 control chromosomes in the GnomAD database, including 56,354 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 0.86 ( 56354 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

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 = 0.977 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:

0.855

AC:

130077

AN:

152112

Hom.:

56302

Cov.:

show subpopulations

Gnomad AFR

AF:

0.701

Gnomad AMI

AF:

0.941

Gnomad AMR

AF:

0.918

Gnomad ASJ

AF:

0.856

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.905

Gnomad FIN

AF:

0.917

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.909

Gnomad OTH

AF:

0.872

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

GnomAD4 genome

AF:

0.855

AC:

130182

AN:

152228

Hom.:

56354

Cov.:

AF XY:

0.859

AC XY:

63918

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.702

Gnomad4 AMR

AF:

0.918

Gnomad4 ASJ

AF:

0.856

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.904

Gnomad4 FIN

AF:

0.917

Gnomad4 NFE

AF:

0.909

Gnomad4 OTH

AF:

0.874

Alfa

AF:

0.898

Hom.:

80109

Bravo

AF:

0.849

Asia WGS

AF:

0.961

AC:

3341

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.14

DANN

Benign

0.36

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