rs836479

Variant names:

• chr7-6391789-C-A
• rs836479
• NM_006908.5:c.108-135C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-6391789-C-A
• chr7-6391789-C-G
• chr7-6391789-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006908.5(RAC1):​c.108-135C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,410,936 control chromosomes in the GnomAD database, including 18,930 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 0.17 (3595 hom., cov: 32)
  • Exomes 𝑓: 0.10 (15335 hom.)
• Consequence: RAC1 NM_006908.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAC1	NM_006908.5	c.108-135C>A		intron_variant	Intron 2 of 5	ENST00000348035.9	NP_008839.2
RAC1	NM_018890.4	c.108-135C>A		intron_variant	Intron 2 of 6		NP_061485.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAC1	ENST00000348035.9	c.108-135C>A		intron_variant	Intron 2 of 5	1	NM_006908.5	ENSP00000258737.7

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26403 AN: 151942 Hom.: 3565 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.177

GnomAD4 exome AF: 0.104 AC: 131545 AN: 1258876 Hom.: 15335 AF XY: 0.107 AC XY: 66414 AN XY: 619246

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.398

Gnomad4 ASJ exome AF: 0.104

Gnomad4 EAS exome AF: 0.594

Gnomad4 SAS exome AF: 0.269

Gnomad4 FIN exome AF: 0.121

Gnomad4 NFE exome AF: 0.0610

Gnomad4 OTH exome AF: 0.135

GnomAD4 genome AF: 0.174 AC: 26487 AN: 152060 Hom.: 3595 Cov.: 32 AF XY: 0.186 AC XY: 13804 AN XY: 74308

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.184

Alfa AF: 0.0798 Hom.: 380

Bravo AF: 0.189

Asia WGS AF: 0.445 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.97
DANN	Benign	0.66

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

Other links and lift over

dbSNP: rs836479; hg19: chr7-6431420;