Variant rs4805110 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 0.805 in 152,142 control chromosomes in the GnomAD database, including 49,419 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 0.81 ( 49419 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0750

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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 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:

0.805

AC:

122370

AN:

152024

Hom.:

49367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.845

Gnomad AMI

AF:

0.773

Gnomad AMR

AF:

0.834

Gnomad ASJ

AF:

0.691

Gnomad EAS

AF:

0.707

Gnomad SAS

AF:

0.810

Gnomad FIN

AF:

0.769

Gnomad MID

AF:

0.693

Gnomad NFE

AF:

0.794

Gnomad OTH

AF:

0.784

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

GnomAD4 genome

AF:

0.805

AC:

122485

AN:

152142

Hom.:

49419

Cov.:

AF XY:

0.803

AC XY:

59717

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.845

Gnomad4 AMR

AF:

0.834

Gnomad4 ASJ

AF:

0.691

Gnomad4 EAS

AF:

0.707

Gnomad4 SAS

AF:

0.810

Gnomad4 FIN

AF:

0.769

Gnomad4 NFE

AF:

0.794

Gnomad4 OTH

AF:

0.784

Alfa

AF:

0.785

Hom.:

47156

Bravo

AF:

0.810

Asia WGS

AF:

0.789

AC:

2746

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.6

DANN

Benign

0.63

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