rs1856651648

Variant names:

• chr11-82982184-G-A
• rs1856651648
• NM_001286060.2:c.593C>T
• RAB30 p.Thr198Ile

Your query was ambiguous. Multiple possible variants found:

• chr11-82982184-G-A
• chr11-82982184-G-C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001286060.2(RAB30):​c.593C>T​(p.Thr198Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T198S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RAB30 NM_001286060.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.63
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.23754784).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286060.2. 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
	RAB30	NM_001286060.2	MANE Select	c.593C>T	p.Thr198Ile	missense	Exon 5 of 5	NP_001272989.1	Q15771-1
	RAB30	NM_001286059.2		c.593C>T	p.Thr198Ile	missense	Exon 5 of 5	NP_001272988.1	Q15771-1
	RAB30	NM_001286061.1		c.593C>T	p.Thr198Ile	missense	Exon 5 of 5	NP_001272990.1	A8K5R1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB30	ENST00000527633.6	TSL:1 MANE Select	c.593C>T	p.Thr198Ile	missense	Exon 5 of 5	ENSP00000435089.1	Q15771-1
	RAB30	ENST00000533486.5	TSL:1	c.593C>T	p.Thr198Ile	missense	Exon 6 of 6	ENSP00000435189.1	Q15771-1
	RAB30	ENST00000534141.5	TSL:1	c.*94C>T		3_prime_UTR	Exon 5 of 5	ENSP00000434974.1	Q15771-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000370 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Benign	-0.037	T
BayesDel_noAF	Benign	-0.29
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.081	T
Eigen	Benign	-0.082
Eigen_PC	Benign	0.17
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.89	D
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.24	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.0	N
PhyloP100		3.6
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	-1.6	N
REVEL	Benign	0.12
Sift	Uncertain	0.017	D
Sift4G	Uncertain	0.037	D
Varity_R		0.11
gMVP		0.45
Mutation Taster		=78/22	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1856651648;

hg19: chr11-82693226;