rs1316252562

Variant names:

• chr1-170532162-C-G
• rs1316252562
• ENST00000367762:c.-62C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-170532162-C-G
• chr1-170532162-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000367762(GORAB):​c.-62C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: GORAB ENST00000367762 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

GORAB (HGNC:25676): (golgin, RAB6 interacting) This gene encodes a member of the golgin family, a group of coiled-coil proteins localized to the Golgi. The encoded protein may function in the secretory pathway. The encoded protein, which also localizes to the cytoplasm, was identified by interactions with the N-terminal kinase-like protein, and thus it may function in mitosis. Mutations in this gene have been associated with geroderma osteodysplastica. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]

GORAB-AS1 (HGNC:54051): (GORAB antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08829051).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GORAB	NM_152281.3	c.-62C>G		upstream_gene_variant		ENST00000367763.8	NP_689494.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GORAB	ENST00000367763.8	c.-62C>G		upstream_gene_variant		2	NM_152281.3	ENSP00000356737.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.032	T
BayesDel_noAF	Benign	-0.28
CADD	Benign	1.2
DANN	Benign	0.95
DEOGEN2	Benign	0.019	T;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.42	T;T
M_CAP	Uncertain	0.15	D
MetaRNN	Benign	0.088	T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.20	N;N
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-0.030	N;N
REVEL	Benign	0.070
Sift	Benign	0.064	T;T
Sift4G	Benign	0.081	T;T
Polyphen		0.0020	B;B
Vest4		0.19
MutPred		0.32		Gain of catalytic residue at A5 (P = 0.0558);Gain of catalytic residue at A5 (P = 0.0558);
MVP		0.36
MPC		0.14
ClinPred		0.21	T
GERP RS		-4.0
Varity_R		0.051
gMVP		0.055

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: rs1316252562; hg19: chr1-170501303;