rs11126375

chr2-26121918-G-A

Variant summary

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

The NM_016131.5(RAB10):c.328-5226G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,106 control chromosomes in the GnomAD database, including 44,761 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 0.77 (44761 hom., cov: 31)
• Consequence: RAB10 NM_016131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

RAB10 (HGNC:9759): (RAB10, member RAS oncogene family) RAB10 belongs to the RAS (see HRAS; MIM 190020) superfamily of small GTPases. RAB proteins localize to exocytic and endocytic compartments and regulate intracellular vesicle trafficking (Bao et al., 1998 [PubMed 9918381]).[supplied by OMIM, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB10	NM_016131.5	c.328-5226G>A		intron_variant		ENST00000264710.5
RAB10	XM_047443004.1	c.313-5226G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB10	ENST00000264710.5	c.328-5226G>A		intron_variant		1	NM_016131.5	P1
RAB10	ENST00000462003.5	n.249-5226G>A		intron_variant, non_coding_transcript_variant		4
RAB10	ENST00000473035.1	n.249-5226G>A		intron_variant, non_coding_transcript_variant		4
RAB10	ENST00000495146.5	n.691-5226G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116557 AN: 151988 Hom.: 44746 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.767 AC: 116615 AN: 152106 Hom.: 44761 Cov.: 31 AF XY: 0.767 AC XY: 56977 AN XY: 74328

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.759

Alfa AF: 0.776 Hom.: 42869

Bravo AF: 0.763

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.6
Dann	Benign	0.63
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs11126375; hg19: chr2-26344787;