rs511145

Variant names:

• chr20-58328842-A-C
• rs511145
• NM_020673.3:c.117-14876A>C

Your query was ambiguous. Multiple possible variants found:

• chr20-58328842-A-C
• chr20-58328842-A-G
• chr20-58328842-A-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.117-14876A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,850 control chromosomes in the GnomAD database, including 22,995 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 0.53 (22995 hom., cov: 31)
• Consequence: RAB22A NM_020673.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB22A	NM_020673.3	c.117-14876A>C		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.117-14876A>C		intron_variant	Intron 2 of 6	1	NM_020673.3	ENSP00000244040.3
RAB22A	ENST00000488949.1	n.336-14876A>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80904 AN: 151734 Hom.: 22940 Cov.: 31

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.534 AC: 81016 AN: 151850 Hom.: 22995 Cov.: 31 AF XY: 0.537 AC XY: 39857 AN XY: 74176

African (AFR) AF: 0.728 AC: 30162 AN: 41406

American (AMR) AF: 0.489 AC: 7467 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3470

East Asian (EAS) AF: 0.460 AC: 2364 AN: 5134

South Asian (SAS) AF: 0.677 AC: 3258 AN: 4812

European-Finnish (FIN) AF: 0.459 AC: 4824 AN: 10510

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29717 AN: 67934

Other (OTH) AF: 0.493 AC: 1039 AN: 2108

Alfa AF: 0.479 Hom.: 9568

Bravo AF: 0.541

Asia WGS AF: 0.571 AC: 1981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.69
DANN	Benign	0.74
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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: rs511145; hg19: chr20-56903898;