rs10890784

Positions:

• chr11-107954513-G-A
• chr11-107954513-G-C

Variant summary

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

The NM_017516.3(RAB39A):​c.228-7433G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,912 control chromosomes in the GnomAD database, including 7,723 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 0.31 (7723 hom., cov: 31)
• Consequence: RAB39A NM_017516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

RAB39A (HGNC:16521): (RAB39A, member RAS oncogene family) Predicted to enable GTPase activity. Involved in phagosome acidification and phagosome-lysosome fusion. Located in 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB39A	NM_017516.3	c.228-7433G>A		intron_variant		ENST00000320578.3	NP_059986.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB39A	ENST00000320578.3	c.228-7433G>A		intron_variant		1	NM_017516.3	ENSP00000322594.2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47603 AN: 151794 Hom.: 7723 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.313 AC: 47623 AN: 151912 Hom.: 7723 Cov.: 31 AF XY: 0.314 AC XY: 23302 AN XY: 74226

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.275

Alfa AF: 0.249 Hom.: 905

Bravo AF: 0.297

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.087
DANN	Benign	0.71

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: rs10890784; hg19: chr11-107825239;