chr13-110546112-C-T

Position:

• chr13-110546112-C-T

Variant summary

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

The NM_017817.3(RAB20):​c.172+15236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0814 in 152,156 control chromosomes in the GnomAD database, including 668 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 0.081 (668 hom., cov: 32)
• Consequence: RAB20 NM_017817.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

RAB20 (HGNC:18260): (RAB20, member RAS oncogene family) Predicted to enable GTPase activity. Involved in phagosome acidification and phagosome-lysosome fusion. Located in Golgi apparatus and phagocytic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB20	NM_017817.3	c.172+15236G>A		intron_variant		ENST00000267328.5	NP_060287.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB20	ENST00000267328.5	c.172+15236G>A		intron_variant		1	NM_017817.3	ENSP00000267328	P1

Frequencies

GnomAD3 genomes AF: 0.0815 AC: 12397 AN: 152038 Hom.: 668 Cov.: 32

Gnomad AFR AF: 0.0197

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.0918

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0814 AC: 12390 AN: 152156 Hom.: 668 Cov.: 32 AF XY: 0.0830 AC XY: 6175 AN XY: 74390

Gnomad4 AFR AF: 0.0196

Gnomad4 AMR AF: 0.0550

Gnomad4 ASJ AF: 0.0983

Gnomad4 EAS AF: 0.0918

Gnomad4 SAS AF: 0.0557

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0615

Alfa AF: 0.0969 Hom.: 1071

Bravo AF: 0.0686

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
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: rs11617401; hg19: chr13-111198459;