rs565990

Variant names:

• chr20-58327363-G-A
• rs565990
• NM_020673.3:c.116+16241G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-58327363-G-A
• chr20-58327363-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RAB22A	NM_020673.3	c.116+16241G>A		intron_variant	Intron 2 of 6	ENST00000244040.4	NP_065724.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB22A	ENST00000244040.4	c.116+16241G>A		intron_variant	Intron 2 of 6	1	NM_020673.3	ENSP00000244040.3
RAB22A	ENST00000488949.1	n.335+16241G>A		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.0105 AC: 437 AN: 41548

American (AMR) AF: 0.0402 AC: 614 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0313 AC: 151 AN: 4832

European-Finnish (FIN) AF: 0.0390 AC: 414 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0556 AC: 3780 AN: 68030

Other (OTH) AF: 0.0426 AC: 90 AN: 2114

Alfa AF: 0.0450 Hom.: 95

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
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs565990; hg19: chr20-56902419;