rs10065350

chr5-58786896-C-T

Variant summary

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

The NM_138453.4(RAB3C):c.372-38142C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 152,024 control chromosomes in the GnomAD database, including 847 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 0.093 (847 hom., cov: 31)
• Consequence: RAB3C NM_138453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

Genes affected

RAB3C (HGNC:30269): (RAB3C, member RAS oncogene family) This gene is a member of the RAS oncogene family and encodes a small GTPase. Other similar small GTPases are known to be involved in vesicle trafficking, and the encoded protein was shown to play a role in recycling phagocytosed MHC class 1 complexes to the cell surface. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB3C	NM_138453.4	c.372-38142C>T		intron_variant		ENST00000282878.6
RAB3C	NM_001317915.2	c.366-38142C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB3C	ENST00000282878.6	c.372-38142C>T		intron_variant		1	NM_138453.4	P1
	ENST00000509476.1	n.221+27764G>A		intron_variant, non_coding_transcript_variant		3
RAB3C	ENST00000507977.1	n.349-7394C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0930 AC: 14124 AN: 151906 Hom.: 843 Cov.: 31

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0769

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0715

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0930 AC: 14137 AN: 152024 Hom.: 847 Cov.: 31 AF XY: 0.0885 AC XY: 6573 AN XY: 74308

Gnomad4 AFR AF: 0.0245

Gnomad4 AMR AF: 0.0870

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0770

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0715

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.112

Alfa AF: 0.125 Hom.: 286

Bravo AF: 0.0909

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.0
Dann	Benign	0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs10065350; hg19: chr5-58082723;