rs2280673

Positions:

• chr3-133839310-A-C
• chr3-133839310-A-G
• chr3-133839310-A-T

Variant summary

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

The NM_016577.4(RAB6B):​c.401+196T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,180 control chromosomes in the GnomAD database, including 27,839 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 0.60 (27839 hom., cov: 34)
• Consequence: RAB6B NM_016577.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

Genes affected

RAB6B (HGNC:14902): (RAB6B, member RAS oncogene family) Enables myosin V binding activity. Predicted to be involved in Golgi vesicle transport; intracellular protein transport; and retrograde transport, endosome to Golgi. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB6B	NM_016577.4	c.401+196T>G		intron_variant		ENST00000285208.9
RAB6B	NM_001363953.1	c.362+196T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB6B	ENST00000285208.9	c.401+196T>G		intron_variant		1	NM_016577.4	P1

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91198 AN: 152062 Hom.: 27837 Cov.: 34

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.600 AC: 91235 AN: 152180 Hom.: 27839 Cov.: 34 AF XY: 0.592 AC XY: 44054 AN XY: 74410

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.584

Alfa AF: 0.626 Hom.: 38446

Bravo AF: 0.586

Asia WGS AF: 0.448 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.11
DANN	Benign	0.67

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: rs2280673; hg19: chr3-133558154;