rs5756573

chr22-37237735-G-A

Variant summary

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

The NM_002872.5(RAC2):c.107+3852C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,070 control chromosomes in the GnomAD database, including 2,134 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 0.14 (2134 hom., cov: 31)
• Consequence: RAC2 NM_002872.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAC2	NM_002872.5	c.107+3852C>T		intron_variant		ENST00000249071.11
RAC2	XM_006724286.4	c.107+3852C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAC2	ENST00000249071.11	c.107+3852C>T		intron_variant		1	NM_002872.5	P1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22040 AN: 151952 Hom.: 2139 Cov.: 31

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.145 AC: 22027 AN: 152070 Hom.: 2134 Cov.: 31 AF XY: 0.153 AC XY: 11368 AN XY: 74326

Gnomad4 AFR AF: 0.0301

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.145

Alfa AF: 0.157 Hom.: 2831

Bravo AF: 0.137

Asia WGS AF: 0.274 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.0
Dann	Benign	0.79

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: rs5756573; hg19: chr22-37633775;