chr11-83012030-T-C

Variant names:

• chr11-83012030-T-C
• rs11233413
• NM_001286060.2:c.-8-14706A>G

Variant summary

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

The NM_001286060.2(RAB30):​c.-8-14706A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,012 control chromosomes in the GnomAD database, including 6,007 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 0.27 (6007 hom., cov: 32)
• Consequence: RAB30 NM_001286060.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 6 publications found

Genes affected

RAB30 (HGNC:9770): (RAB30, member RAS oncogene family) Predicted to enable GTP binding activity and GTPase activity. Involved in Golgi organization. Located in Golgi cisterna; cis-Golgi network; and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000254698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB30	NM_001286060.2	c.-8-14706A>G		intron_variant	Intron 1 of 4	ENST00000527633.6	NP_001272989.1
RAB30	NM_001286059.2	c.-8-14706A>G		intron_variant	Intron 1 of 4		NP_001272988.1
RAB30	NM_001286061.1	c.-8-14706A>G		intron_variant	Intron 1 of 4		NP_001272990.1
RAB30	NM_014488.5	c.-8-14706A>G		intron_variant	Intron 2 of 5		NP_055303.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB30	ENST00000527633.6	c.-8-14706A>G		intron_variant	Intron 1 of 4	1	NM_001286060.2	ENSP00000435089.1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41108 AN: 151894 Hom.: 5999 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.271 AC: 41146 AN: 152012 Hom.: 6007 Cov.: 32 AF XY: 0.274 AC XY: 20333 AN XY: 74272

African (AFR) AF: 0.158 AC: 6541 AN: 41480

American (AMR) AF: 0.311 AC: 4751 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1489 AN: 5168

South Asian (SAS) AF: 0.281 AC: 1351 AN: 4814

European-Finnish (FIN) AF: 0.386 AC: 4069 AN: 10530

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.307 AC: 20840 AN: 67964

Other (OTH) AF: 0.277 AC: 585 AN: 2110

Alfa AF: 0.292 Hom.: 20613

Bravo AF: 0.259

Asia WGS AF: 0.279 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	17
DANN	Benign	0.90
PhyloP100		1.5
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: rs11233413; hg19: chr11-82723072;