rs2105601

Variant names:

• chr11-87955673-T-C
• rs2105601
• ENST00000649399.1:n.33-767A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-87955673-T-C
• chr11-87955673-T-G

Variant summary

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

The ENST00000649399.1(ENSG00000285835):​n.33-767A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 139,514 control chromosomes in the GnomAD database, including 427 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 0.068 (427 hom., cov: 31)
• Consequence: ENSG00000285835 ENST00000649399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 1 publications found

Genes affected

ENSG00000285835 (HGNC:):

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB38	XM_017017455.3	c.484-767A>G		intron_variant	Intron 2 of 3		XP_016872944.1
RAB38	XM_017017456.3	c.484-767A>G		intron_variant	Intron 2 of 3		XP_016872945.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285835	ENST00000649399.1	n.33-767A>G		intron_variant	Intron 1 of 3
ENSG00000294816	ENST00000726097.1	n.578-4081T>C		intron_variant	Intron 5 of 5
ENSG00000294816	ENST00000726098.1	n.472-4081T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 9504 AN: 139442 Hom.: 428 Cov.: 31

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.0343

Gnomad AMR AF: 0.0540

Gnomad ASJ AF: 0.0728

Gnomad EAS AF: 0.000535

Gnomad SAS AF: 0.0264

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0965

Gnomad OTH AF: 0.0582

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

GnomAD4 genome AF: 0.0681 AC: 9502 AN: 139514 Hom.: 427 Cov.: 31 AF XY: 0.0678 AC XY: 4621 AN XY: 68136

African (AFR) AF: 0.0176 AC: 642 AN: 36402

American (AMR) AF: 0.0540 AC: 781 AN: 14472

Ashkenazi Jewish (ASJ) AF: 0.0728 AC: 248 AN: 3408

East Asian (EAS) AF: 0.000536 AC: 2 AN: 3732

South Asian (SAS) AF: 0.0269 AC: 118 AN: 4390

European-Finnish (FIN) AF: 0.138 AC: 1346 AN: 9758

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0965 AC: 6202 AN: 64246

Other (OTH) AF: 0.0574 AC: 113 AN: 1968

Alfa AF: 0.0616 Hom.: 325

Bravo AF: 0.0542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.63
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2105601; hg19: chr11-87666565;