chr20-58327363-G-A

Position:

• chr20-58327363-G-A

Variant summary

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

The NM_020673.3(RAB22A):​c.116+16241G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 152,274 control chromosomes in the GnomAD database, including 154 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 0.037 (154 hom., cov: 32)
• Consequence: RAB22A NM_020673.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

Genes affected

RAB22A (HGNC:9764): (RAB22A, member RAS oncogene family) The protein encoded by this gene is a member of the RAB family of small GTPases. The GTP-bound form of the encoded protein has been shown to interact with early-endosomal antigen 1, and may be involved in the trafficking of and interaction between endosomal compartments. [provided by RefSeq, Jul 2008]

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 (NFE) allele frequency at 95% confidence interval = 0.0541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB22A	NM_020673.3	c.116+16241G>A		intron_variant		ENST00000244040.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB22A	ENST00000244040.4	c.116+16241G>A		intron_variant		1	NM_020673.3	P1
RAB22A	ENST00000488949.1	n.335+16241G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0372 AC: 5653 AN: 152156 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0402

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0556

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0371 AC: 5654 AN: 152274 Hom.: 154 Cov.: 32 AF XY: 0.0361 AC XY: 2686 AN XY: 74452

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.0402

Gnomad4 ASJ AF: 0.0392

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0313

Gnomad4 FIN AF: 0.0390

Gnomad4 NFE AF: 0.0556

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0439 Hom.: 84

Bravo AF: 0.0360

Asia WGS AF: 0.0190 AC: 65 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	0.69
DANN	Benign	0.23

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: rs565990; hg19: chr20-56902419;