Variant rs1268843 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 0.733 in 152,190 control chromosomes in the GnomAD database, including 41,066 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 0.73 ( 41066 hom., cov: 34)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.529

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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.761 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:

0.733

AC:

111538

AN:

152072

Hom.:

41027

Cov.:

show subpopulations

Gnomad AFR

AF:

0.768

Gnomad AMI

AF:

0.748

Gnomad AMR

AF:

0.691

Gnomad ASJ

AF:

0.657

Gnomad EAS

AF:

0.723

Gnomad SAS

AF:

0.782

Gnomad FIN

AF:

0.700

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.728

Gnomad OTH

AF:

0.733

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

GnomAD4 genome

AF:

0.733

AC:

111631

AN:

152190

Hom.:

41066

Cov.:

AF XY:

0.729

AC XY:

54262

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.768

Gnomad4 AMR

AF:

0.692

Gnomad4 ASJ

AF:

0.657

Gnomad4 EAS

AF:

0.723

Gnomad4 SAS

AF:

0.781

Gnomad4 FIN

AF:

0.700

Gnomad4 NFE

AF:

0.728

Gnomad4 OTH

AF:

0.734

Alfa

AF:

0.724

Hom.:

59156

Bravo

AF:

0.739

Asia WGS

AF:

0.742

AC:

2582

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.9

DANN

Benign

0.61

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