rs511145

chr20-58328842-A-Cchr20-58328842-A-Gchr20-58328842-A-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• 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/exons	MANE	UniProt
RAB22A	NM_020673.3	c.117-14876A>C		intron_variant		ENST00000244040.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB22A	ENST00000244040.4	c.117-14876A>C		intron_variant		1	NM_020673.3	P1
RAB22A	ENST00000488949.1	n.336-14876A>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.493

Alfa AF: 0.478 Hom.: 8524

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

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: rs511145; hg19: chr20-56903898;