Variant rs2313475 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 0.704 in 152,106 control chromosomes in the GnomAD database, including 38,621 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 0.70 ( 38621 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80

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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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:

0.704

AC:

107045

AN:

151988

Hom.:

38601

Cov.:

show subpopulations

Gnomad AFR

AF:

0.558

Gnomad AMI

AF:

0.779

Gnomad AMR

AF:

0.771

Gnomad ASJ

AF:

0.672

Gnomad EAS

AF:

0.974

Gnomad SAS

AF:

0.797

Gnomad FIN

AF:

0.837

Gnomad MID

AF:

0.775

Gnomad NFE

AF:

0.730

Gnomad OTH

AF:

0.705

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

GnomAD4 genome

AF:

0.704

AC:

107106

AN:

152106

Hom.:

38621

Cov.:

AF XY:

0.714

AC XY:

53111

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.558

Gnomad4 AMR

AF:

0.772

Gnomad4 ASJ

AF:

0.672

Gnomad4 EAS

AF:

0.974

Gnomad4 SAS

AF:

0.798

Gnomad4 FIN

AF:

0.837

Gnomad4 NFE

AF:

0.730

Gnomad4 OTH

AF:

0.707

Alfa

AF:

0.728

Hom.:

52519

Bravo

AF:

0.695

Asia WGS

AF:

0.858

AC:

2984

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.20

DANN

Benign

0.60

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