Variant rs485916 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 0.587 in 151,982 control chromosomes in the GnomAD database, including 27,117 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 0.59 ( 27117 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.288

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 (EAS) allele frequency at 95% confidence interval = 0.746 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:

0.586

AC:

89064

AN:

151864

Hom.:

27082

Cov.:

show subpopulations

Gnomad AFR

AF:

0.737

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.583

Gnomad ASJ

AF:

0.427

Gnomad EAS

AF:

0.767

Gnomad SAS

AF:

0.606

Gnomad FIN

AF:

0.532

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.500

Gnomad OTH

AF:

0.533

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

GnomAD4 genome

AF:

0.587

AC:

89154

AN:

151982

Hom.:

27117

Cov.:

AF XY:

0.589

AC XY:

43761

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.738

Gnomad4 AMR

AF:

0.583

Gnomad4 ASJ

AF:

0.427

Gnomad4 EAS

AF:

0.766

Gnomad4 SAS

AF:

0.604

Gnomad4 FIN

AF:

0.532

Gnomad4 NFE

AF:

0.500

Gnomad4 OTH

AF:

0.529

Alfa

AF:

0.507

Hom.:

25726

Bravo

AF:

0.594

Asia WGS

AF:

0.671

AC:

2332

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

2.0

DANN

Benign

0.27

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