Variant chr5-181242275-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006098.5(RACK1):c.180G>A(p.Arg60Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0045 in 1,613,564 control chromosomes in the GnomAD database, including 119 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 63 hom., cov: 33)

Exomes 𝑓: 0.0033 ( 56 hom. )

Consequence

RACK1
NM_006098.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.941

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:

RACK1 (HGNC:):

RACK1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-181242275-C-T is Benign according to our data. Variant chr5-181242275-C-T is described in ClinVar as [Benign]. Clinvar id is 781742.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RACK1	NM_006098.5 linkuse as main transcript	c.180G>A	p.Arg60Arg	synonymous_variant	2/8	ENST00000512805.6	NP_006089.1	P63244E9KL35

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RACK1	ENST00000512805.6 linkuse as main transcript	c.180G>A	p.Arg60Arg	synonymous_variant	2/8	1	NM_006098.5	ENSP00000426909.1		P63244
RACK1	ENST00000376817.8 linkuse as main transcript	c.110-62G>A		intron_variant		5		ENSP00000366013.4		J3KPE3

Frequencies

GnomAD3 genomes

AF:

0.0156

AC:

2377

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0506

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.00497

Gnomad ASJ

AF:

0.00806

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00600

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00162

Gnomad OTH

AF:

0.00860

GnomAD3 exomes

AF:

0.00597

AC:

1500

AN:

251338

Hom.:

AF XY:

0.00529

AC XY:

719

AN XY:

135850

show subpopulations

Gnomad AFR exome

AF:

0.0508

Gnomad AMR exome

AF:

0.00315

Gnomad ASJ exome

AF:

0.0103

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00719

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.00187

Gnomad OTH exome

AF:

0.00456

GnomAD4 exome

AF:

0.00333

AC:

4872

AN:

1461248

Hom.:

Cov.:

AF XY:

0.00335

AC XY:

2439

AN XY:

726990

show subpopulations

Gnomad4 AFR exome

AF:

0.0530

Gnomad4 AMR exome

AF:

0.00333

Gnomad4 ASJ exome

AF:

0.0106

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00667

Gnomad4 FIN exome

AF:

0.000112

Gnomad4 NFE exome

AF:

0.00150

Gnomad4 OTH exome

AF:

0.00614

GnomAD4 genome

AF:

0.0157

AC:

2384

AN:

152316

Hom.:

Cov.:

AF XY:

0.0146

AC XY:

1088

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.0507

Gnomad4 AMR

AF:

0.00497

Gnomad4 ASJ

AF:

0.00806

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00580

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00162

Gnomad4 OTH

AF:

0.00851

Alfa

AF:

0.00886

Hom.:

Bravo

AF:

0.0179

Asia WGS

AF:

0.00346

AC:

AN:

3478

EpiCase

AF:

0.00316

EpiControl

AF:

0.00344

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.69

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.9

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.66

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.66

Position offset: -1

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over