rs4821615

Positions:

• chr22-37250091-G-C

Variant summary

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

The variant allele was found at a frequency of 0.514 in 151,970 control chromosomes in the GnomAD database, including 21,411 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 0.51 (21411 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37250091G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAC2	ENST00000699915.1	n.94-8433C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77988 AN: 151852 Hom.: 21378 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.514 AC: 78082 AN: 151970 Hom.: 21411 Cov.: 32 AF XY: 0.508 AC XY: 37685 AN XY: 74254

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.491

Alfa AF: 0.477 Hom.: 2274

Bravo AF: 0.521

Asia WGS AF: 0.448 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.31
DANN	Benign	0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4821615; hg19: chr22-37646131;