Variant 7-6392059-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006908.5(RAC1):c.225+18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 1,613,614 control chromosomes in the GnomAD database, including 218,566 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.57 ( 26069 hom., cov: 32)

Exomes 𝑓: 0.50 ( 192497 hom. )

Consequence

RAC1
NM_006908.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.39

Variant links:

Genes affected

RAC1 (HGNC:9801): (Rac family small GTPase 1) The protein encoded by this gene is a GTPase which belongs to the RAS superfamily of small GTP-binding proteins. Members of this superfamily appear to regulate a diverse array of cellular events, including the control of cell growth, cytoskeletal reorganization, and the activation of protein kinases. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

RAC1 links:

RAC1 (HGNC:):

RAC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 7-6392059-C-T is Benign according to our data. Variant chr7-6392059-C-T is described in ClinVar as [Benign]. Clinvar id is 1327930.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-6392059-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAC1	NM_006908.5 linkuse as main transcript	c.225+18C>T		intron_variant		ENST00000348035.9	NP_008839.2	P63000-1A4D2P1
RAC1	NM_018890.4 linkuse as main transcript	c.225+18C>T		intron_variant			NP_061485.1	P63000-2A4D2P0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAC1	ENST00000348035.9 linkuse as main transcript	c.225+18C>T		intron_variant		1	NM_006908.5	ENSP00000258737.7		P63000-1

Frequencies

GnomAD3 genomes

AF:

0.570

AC:

86584

AN:

151868

Hom.:

26019

Cov.:

show subpopulations

Gnomad AFR

AF:

0.716

Gnomad AMI

AF:

0.517

Gnomad AMR

AF:

0.625

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.909

Gnomad SAS

AF:

0.640

Gnomad FIN

AF:

0.474

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.466

Gnomad OTH

AF:

0.540

GnomAD3 exomes

AF:

0.562

AC:

141158

AN:

251230

Hom.:

42598

AF XY:

0.551

AC XY:

74788

AN XY:

135808

show subpopulations

Gnomad AFR exome

AF:

0.723

Gnomad AMR exome

AF:

0.704

Gnomad ASJ exome

AF:

0.381

Gnomad EAS exome

AF:

0.911

Gnomad SAS exome

AF:

0.618

Gnomad FIN exome

AF:

0.478

Gnomad NFE exome

AF:

0.459

Gnomad OTH exome

AF:

0.510

GnomAD4 exome

AF:

0.503

AC:

735385

AN:

1461628

Hom.:

192497

Cov.:

AF XY:

0.504

AC XY:

366140

AN XY:

727068

show subpopulations

Gnomad4 AFR exome

AF:

0.725

Gnomad4 AMR exome

AF:

0.694

Gnomad4 ASJ exome

AF:

0.382

Gnomad4 EAS exome

AF:

0.906

Gnomad4 SAS exome

AF:

0.615

Gnomad4 FIN exome

AF:

0.472

Gnomad4 NFE exome

AF:

0.469

Gnomad4 OTH exome

AF:

0.534

GnomAD4 genome

AF:

0.570

AC:

86694

AN:

151986

Hom.:

26069

Cov.:

AF XY:

0.575

AC XY:

42697

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.716

Gnomad4 AMR

AF:

0.625

Gnomad4 ASJ

AF:

0.369

Gnomad4 EAS

AF:

0.909

Gnomad4 SAS

AF:

0.639

Gnomad4 FIN

AF:

0.474

Gnomad4 NFE

AF:

0.466

Gnomad4 OTH

AF:

0.546

Alfa

AF:

0.518

Hom.:

4602

Bravo

AF:

0.590

Asia WGS

AF:

0.809

AC:

2812

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Intellectual disability, autosomal dominant 48

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 07, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

8.4

DANN

Benign

0.87

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over