Variant rs2468475 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 0.422 in 151,882 control chromosomes in the GnomAD database, including 13,929 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 0.42 ( 13929 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.835

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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 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:

0.422

AC:

64043

AN:

151766

Hom.:

13916

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.564

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.472

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.485

Gnomad MID

AF:

0.510

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.465

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

GnomAD4 genome

AF:

0.422

AC:

64086

AN:

151882

Hom.:

13929

Cov.:

AF XY:

0.420

AC XY:

31177

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.353

Gnomad4 AMR

AF:

0.396

Gnomad4 ASJ

AF:

0.472

Gnomad4 EAS

AF:

0.195

Gnomad4 SAS

AF:

0.339

Gnomad4 FIN

AF:

0.485

Gnomad4 NFE

AF:

0.477

Gnomad4 OTH

AF:

0.460

Alfa

AF:

0.442

Hom.:

10561

Bravo

AF:

0.413

Asia WGS

AF:

0.282

AC:

984

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

5.6

DANN

Benign

0.35

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