Variant rs899435 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 0.531 in 152,062 control chromosomes in the GnomAD database, including 21,941 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 0.53 ( 21941 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.752

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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:

0.531

AC:

80722

AN:

151944

Hom.:

21932

Cov.:

show subpopulations

Gnomad AFR

AF:

0.565

Gnomad AMI

AF:

0.492

Gnomad AMR

AF:

0.468

Gnomad ASJ

AF:

0.475

Gnomad EAS

AF:

0.215

Gnomad SAS

AF:

0.521

Gnomad FIN

AF:

0.497

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.558

Gnomad OTH

AF:

0.545

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

GnomAD4 genome

AF:

0.531

AC:

80756

AN:

152062

Hom.:

21941

Cov.:

AF XY:

0.524

AC XY:

38997

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.565

Gnomad4 AMR

AF:

0.467

Gnomad4 ASJ

AF:

0.475

Gnomad4 EAS

AF:

0.215

Gnomad4 SAS

AF:

0.521

Gnomad4 FIN

AF:

0.497

Gnomad4 NFE

AF:

0.558

Gnomad4 OTH

AF:

0.544

Alfa

AF:

0.379

Hom.:

957

Bravo

AF:

0.529

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.54

DANN

Benign

0.66

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