Variant rs859665 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 0.388 in 151,870 control chromosomes in the GnomAD database, including 12,911 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 0.39 ( 12911 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.591

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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 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:

0.388

AC:

58837

AN:

151752

Hom.:

12901

Cov.:

show subpopulations

Gnomad AFR

AF:

0.583

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.00889

Gnomad SAS

AF:

0.248

Gnomad FIN

AF:

0.303

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.364

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

GnomAD4 genome

AF:

0.388

AC:

58871

AN:

151870

Hom.:

12911

Cov.:

AF XY:

0.380

AC XY:

28209

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.583

Gnomad4 AMR

AF:

0.310

Gnomad4 ASJ

AF:

0.355

Gnomad4 EAS

AF:

0.00891

Gnomad4 SAS

AF:

0.247

Gnomad4 FIN

AF:

0.303

Gnomad4 NFE

AF:

0.341

Gnomad4 OTH

AF:

0.358

Alfa

AF:

0.322

Hom.:

4699

Bravo

AF:

0.399

Asia WGS

AF:

0.151

AC:

529

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

0.38

DANN

Benign

0.55

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