Variant 7-6387310-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.107+27C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 1,442,870 control chromosomes in the GnomAD database, including 199,993 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.60 ( 29343 hom., cov: 33)

Exomes 𝑓: 0.50 ( 170650 hom. )

Consequence

RAC1
NM_006908.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.769

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=-0.87).

BP6

Variant 7-6387310-C-T is Benign according to our data. Variant chr7-6387310-C-T is described in ClinVar as [Benign]. Clinvar id is 1327929.Status of the report is criteria_provided_single_submitter, 1 stars.

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.107+27C>T		intron_variant		ENST00000348035.9	NP_008839.2	P63000-1A4D2P1
RAC1	NM_018890.4 linkuse as main transcript	c.107+27C>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.107+27C>T		intron_variant		1	NM_006908.5	ENSP00000258737.7		P63000-1

Frequencies

GnomAD3 genomes

AF:

0.598

AC:

90919

AN:

151976

Hom.:

29276

Cov.:

show subpopulations

Gnomad AFR

AF:

0.814

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.635

Gnomad ASJ

AF:

0.374

Gnomad EAS

AF:

0.909

Gnomad SAS

AF:

0.640

Gnomad FIN

AF:

0.475

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.466

Gnomad OTH

AF:

0.559

GnomAD3 exomes

AF:

0.543

AC:

112942

AN:

207992

Hom.:

33364

AF XY:

0.532

AC XY:

60623

AN XY:

113952

show subpopulations

Gnomad AFR exome

AF:

0.812

Gnomad AMR exome

AF:

0.674

Gnomad ASJ exome

AF:

0.369

Gnomad EAS exome

AF:

0.903

Gnomad SAS exome

AF:

0.605

Gnomad FIN exome

AF:

0.473

Gnomad NFE exome

AF:

0.447

Gnomad OTH exome

AF:

0.491

GnomAD4 exome

AF:

0.503

AC:

649201

AN:

1290776

Hom.:

170650

Cov.:

AF XY:

0.503

AC XY:

326689

AN XY:

648906

show subpopulations

Gnomad4 AFR exome

AF:

0.818

Gnomad4 AMR exome

AF:

0.669

Gnomad4 ASJ exome

AF:

0.380

Gnomad4 EAS exome

AF:

0.904

Gnomad4 SAS exome

AF:

0.610

Gnomad4 FIN exome

AF:

0.471

Gnomad4 NFE exome

AF:

0.469

Gnomad4 OTH exome

AF:

0.537

GnomAD4 genome

AF:

0.599

AC:

91048

AN:

152094

Hom.:

29343

Cov.:

AF XY:

0.602

AC XY:

44764

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.814

Gnomad4 AMR

AF:

0.636

Gnomad4 ASJ

AF:

0.374

Gnomad4 EAS

AF:

0.909

Gnomad4 SAS

AF:

0.639

Gnomad4 FIN

AF:

0.475

Gnomad4 NFE

AF:

0.466

Gnomad4 OTH

AF:

0.565

Alfa

AF:

0.499

Hom.:

3654

Bravo

AF:

0.621

Asia WGS

AF:

0.816

AC:

2834

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

-0.87

CADD

Benign

2.0

DANN

Benign

0.57

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