NM_017817.3:c.173-14869T>C

Variant names:

• chr13-110539066-A-G
• rs2148079
• NM_017817.3:c.173-14869T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017817.3(RAB20):​c.173-14869T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,110 control chromosomes in the GnomAD database, including 10,099 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 0.34 (10099 hom., cov: 33)
• Consequence: RAB20 NM_017817.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB20	NM_017817.3	c.173-14869T>C		intron_variant	Intron 1 of 1	ENST00000267328.5	NP_060287.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB20	ENST00000267328.5	c.173-14869T>C		intron_variant	Intron 1 of 1	1	NM_017817.3	ENSP00000267328.3

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52103 AN: 151992 Hom.: 10078 Cov.: 33

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.343 AC: 52168 AN: 152110 Hom.: 10099 Cov.: 33 AF XY: 0.340 AC XY: 25285 AN XY: 74352

African (AFR) AF: 0.526 AC: 21815 AN: 41482

American (AMR) AF: 0.268 AC: 4099 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1087 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1871 AN: 5178

South Asian (SAS) AF: 0.302 AC: 1459 AN: 4824

European-Finnish (FIN) AF: 0.214 AC: 2265 AN: 10582

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18339 AN: 67974

Other (OTH) AF: 0.332 AC: 701 AN: 2112

Alfa AF: 0.315 Hom.: 1094

Bravo AF: 0.354

Asia WGS AF: 0.333 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.45
PhyloP100		0.35
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: rs2148079; hg19: chr13-111191413;