Variant rs4453140 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 0.77 in 151,968 control chromosomes in the GnomAD database, including 45,382 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 0.77 ( 45382 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539

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=-1.02).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 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:

0.770

AC:

116937

AN:

151850

Hom.:

45383

Cov.:

show subpopulations

Gnomad AFR

AF:

0.679

Gnomad AMI

AF:

0.781

Gnomad AMR

AF:

0.729

Gnomad ASJ

AF:

0.784

Gnomad EAS

AF:

0.797

Gnomad SAS

AF:

0.752

Gnomad FIN

AF:

0.860

Gnomad MID

AF:

0.829

Gnomad NFE

AF:

0.818

Gnomad OTH

AF:

0.797

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

GnomAD4 genome

AF:

0.770

AC:

116973

AN:

151968

Hom.:

45382

Cov.:

AF XY:

0.771

AC XY:

57256

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.679

Gnomad4 AMR

AF:

0.728

Gnomad4 ASJ

AF:

0.784

Gnomad4 EAS

AF:

0.796

Gnomad4 SAS

AF:

0.752

Gnomad4 FIN

AF:

0.860

Gnomad4 NFE

AF:

0.818

Gnomad4 OTH

AF:

0.793

Alfa

AF:

0.769

Hom.:

5459

Bravo

AF:

0.754

Asia WGS

AF:

0.750

AC:

2610

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

0.95

DANN

Benign

0.082

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