11-88086259-T-C

Variant names:

• chr11-88086259-T-C
• rs1386330
• XM_017017455.3:c.483+63416A>G

Variant summary

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

The XM_017017455.3(RAB38):​c.483+63416A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 151,944 control chromosomes in the GnomAD database, including 1,392 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 0.13 (1392 hom., cov: 32)
• Consequence: RAB38 XM_017017455.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

Genes affected

RAB38 (HGNC:9776): (RAB38, member RAS oncogene family) Enables several functions, including AP-1 adaptor complex binding activity; AP-3 adaptor complex binding activity; and BLOC-2 complex binding activity. Involved in several processes, including endosome to melanosome transport; melanosome assembly; and phagosome acidification. Located in several cellular components, including cytoplasmic vesicle; lysosome; and mitochondria-associated endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000255102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB38	XM_017017455.3	c.483+63416A>G		intron_variant	Intron 2 of 3		XP_016872944.1
RAB38	XM_017017456.3	c.483+63416A>G		intron_variant	Intron 2 of 3		XP_016872945.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255102	ENST00000531454.1	n.236+11653A>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19511 AN: 151826 Hom.: 1394 Cov.: 32

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0765

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0688

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.128 AC: 19524 AN: 151944 Hom.: 1392 Cov.: 32 AF XY: 0.126 AC XY: 9395 AN XY: 74278

Gnomad4 AFR AF: 0.0902

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0767

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0688

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.133

Alfa AF: 0.134 Hom.: 1441

Bravo AF: 0.137

Asia WGS AF: 0.118 AC: 410 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1386330; hg19: chr11-87819427;