Variant rs3756585 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000510199.5(RACK1):c.254-1684T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 1,391,956 control chromosomes in the GnomAD database, including 7,053 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 0.13 ( 1859 hom., cov: 33)

Exomes 𝑓: 0.075 ( 5194 hom. )

Consequence

RACK1
ENST00000510199.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.54

Variant links:

Genes affected

RACK1 (HGNC:4399): (receptor for activated C kinase 1) Enables several functions, including cyclin binding activity; enzyme binding activity; and protein domain specific binding activity. Involved in several processes, including positive regulation of hydrolase activity; regulation of cellular protein metabolic process; and regulation of signal transduction. Located in several cellular components, including midbody; perinuclear region of cytoplasm; and phagocytic cup. Part of IRE1-RACK1-PP2A complex. [provided by Alliance of Genome Resources, Apr 2022]

RACK1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RACK1	ENST00000507000.5 linkuse as main transcript	c.-14-1684T>G		intron_variant		5
RACK1	ENST00000510199.5 linkuse as main transcript	c.254-1684T>G		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19859

AN:

152194

Hom.:

1843

Cov.:

show subpopulations

Gnomad AFR

AF:

0.244

Gnomad AMI

AF:

0.0932

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.136

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.0594

Gnomad OTH

AF:

0.129

GnomAD4 exome

AF:

0.0748

AC:

92743

AN:

1239644

Hom.:

5194

Cov.:

AF XY:

0.0764

AC XY:

45677

AN XY:

597822

show subpopulations

Gnomad4 AFR exome

AF:

0.254

Gnomad4 AMR exome

AF:

0.107

Gnomad4 ASJ exome

AF:

0.131

Gnomad4 EAS exome

AF:

0.271

Gnomad4 SAS exome

AF:

0.153

Gnomad4 FIN exome

AF:

0.0957

Gnomad4 NFE exome

AF:

0.0556

Gnomad4 OTH exome

AF:

0.101

GnomAD4 genome

AF:

0.131

AC:

19911

AN:

152312

Hom.:

1859

Cov.:

AF XY:

0.133

AC XY:

9908

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.245

Gnomad4 AMR

AF:

0.101

Gnomad4 ASJ

AF:

0.136

Gnomad4 EAS

AF:

0.270

Gnomad4 SAS

AF:

0.161

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.0593

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.111

Hom.:

280

Bravo

AF:

0.138

Asia WGS

AF:

0.229

AC:

797

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

0.37

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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