rs9607431

Variant names:

• chr22-37233898-A-C
• rs9607431
• NM_002872.5:c.108-980T>G

Your query was ambiguous. Multiple possible variants found:

• chr22-37233898-A-C
• chr22-37233898-A-T

Variant summary

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

The NM_002872.5(RAC2):​c.108-980T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,122 control chromosomes in the GnomAD database, including 1,474 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 (1474 hom., cov: 32)
• Consequence: RAC2 NM_002872.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83

Genes affected

RAC2 (HGNC:9802): (Rac family small GTPase 2) This gene encodes a member of the Ras superfamily of small guanosine triphosphate (GTP)-metabolizing proteins. The encoded protein localizes to the plasma membrane, where it regulates diverse processes, such as secretion, phagocytosis, and cell polarization. Activity of this protein is also involved in the generation of reactive oxygen species. Mutations in this gene are associated with neutrophil immunodeficiency syndrome. There is a pseudogene for this gene on chromosome 6. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAC2	NM_002872.5	c.108-980T>G		intron_variant	Intron 2 of 6	ENST00000249071.11	NP_002863.1
RAC2	XM_006724286.4	c.108-980T>G		intron_variant	Intron 2 of 5		XP_006724349.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAC2	ENST00000249071.11	c.108-980T>G		intron_variant	Intron 2 of 6	1	NM_002872.5	ENSP00000249071.6

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20412 AN: 152000 Hom.: 1468 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.144

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.134 AC: 20436 AN: 152122 Hom.: 1474 Cov.: 32 AF XY: 0.135 AC XY: 10007 AN XY: 74366

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0917

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.146

Alfa AF: 0.117 Hom.: 1121

Bravo AF: 0.134

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.7
DANN	Benign	0.74

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: rs9607431; hg19: chr22-37629938;