Variant rs4672448 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 0.863 in 152,202 control chromosomes in the GnomAD database, including 56,714 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 ( 56714 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

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=-1.03).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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:

0.862

AC:

131152

AN:

152084

Hom.:

56645

Cov.:

show subpopulations

Gnomad AFR

AF:

0.826

Gnomad AMI

AF:

0.847

Gnomad AMR

AF:

0.902

Gnomad ASJ

AF:

0.825

Gnomad EAS

AF:

0.934

Gnomad SAS

AF:

0.863

Gnomad FIN

AF:

0.933

Gnomad MID

AF:

0.782

Gnomad NFE

AF:

0.862

Gnomad OTH

AF:

0.856

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

GnomAD4 genome

AF:

0.863

AC:

131282

AN:

152202

Hom.:

56714

Cov.:

AF XY:

0.866

AC XY:

64465

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.826

Gnomad4 AMR

AF:

0.902

Gnomad4 ASJ

AF:

0.825

Gnomad4 EAS

AF:

0.934

Gnomad4 SAS

AF:

0.864

Gnomad4 FIN

AF:

0.933

Gnomad4 NFE

AF:

0.862

Gnomad4 OTH

AF:

0.857

Alfa

AF:

0.863

Hom.:

76758

Bravo

AF:

0.860

Asia WGS

AF:

0.912

AC:

3168

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.1

DANN

Benign

0.16

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