rs2239508

Variant names:

• chr18-9845860-C-A
• rs2239508
• NM_006868.4:c.490+169C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-9845860-C-A
• chr18-9845860-C-G

Variant summary

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

The NM_006868.4(RAB31):​c.490+169C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,048 control chromosomes in the GnomAD database, including 10,731 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 (10731 hom., cov: 33)
• Consequence: RAB31 NM_006868.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616
• Publications: 2 publications found

Genes affected

RAB31 (HGNC:9771): (RAB31, member RAS oncogene family) Enables GDP binding activity and GTP binding activity. Involved in several processes, including Golgi to plasma membrane protein transport; cellular response to insulin stimulus; and receptor internalization. Located in early endosome; phagocytic vesicle; and trans-Golgi network membrane. Biomarker of severe acute respiratory syndrome. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006868.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB31	NM_006868.4	MANE Select	c.490+169C>A		intron	N/A	NP_006859.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB31	ENST00000578921.6	TSL:1 MANE Select	c.490+169C>A		intron	N/A	ENSP00000461945.2
	RAB31	ENST00000948391.1		c.772+169C>A		intron	N/A	ENSP00000618450.1
	RAB31	ENST00000934253.1		c.604+169C>A		intron	N/A	ENSP00000604312.1

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52407 AN: 151930 Hom.: 10735 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.345 AC: 52392 AN: 152048 Hom.: 10731 Cov.: 33 AF XY: 0.352 AC XY: 26190 AN XY: 74326

African (AFR) AF: 0.110 AC: 4584 AN: 41494

American (AMR) AF: 0.447 AC: 6830 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3468

East Asian (EAS) AF: 0.580 AC: 2999 AN: 5172

South Asian (SAS) AF: 0.442 AC: 2129 AN: 4818

European-Finnish (FIN) AF: 0.454 AC: 4801 AN: 10564

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28827 AN: 67946

Other (OTH) AF: 0.336 AC: 709 AN: 2112

Alfa AF: 0.395 Hom.: 19566

Bravo AF: 0.333

Asia WGS AF: 0.477 AC: 1656 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.79
PhyloP100		0.62
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: rs2239508; hg19: chr18-9845857;