13-45486556-C-G

Variant names:

• chr13-45486556-C-G
• NM_031431.4:c.905C>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_031431.4(COG3):​c.905C>G​(p.Ala302Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: COG3 NM_031431.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.67

Genes affected

COG3 (HGNC:18619): (component of oligomeric golgi complex 3) This gene encodes a component of the conserved oligomeric Golgi (COG) complex which is composed of eight different subunits and is required for normal Golgi morphology and localization. Defects in the COG complex result in multiple deficiencies in protein glycosylation. The protein encoded by this gene is involved in ER-Golgi transport.[provided by RefSeq, Jun 2011]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.35540247).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COG3	NM_031431.4	c.905C>G	p.Ala302Gly	missense_variant	Exon 8 of 23	ENST00000349995.10	NP_113619.3
COG3	XM_047430702.1	c.905C>G	p.Ala302Gly	missense_variant	Exon 8 of 19		XP_047286658.1
COG3	XR_007063702.1	n.1003C>G		non_coding_transcript_exon_variant	Exon 8 of 14
COG3	XR_429222.5	n.1003C>G		non_coding_transcript_exon_variant	Exon 8 of 24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COG3	ENST00000349995.10	c.905C>G	p.Ala302Gly	missense_variant	Exon 8 of 23	1	NM_031431.4	ENSP00000258654.8
COG3	ENST00000617493.1	c.905C>G	p.Ala302Gly	missense_variant	Exon 8 of 12	1		ENSP00000481332.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Feb 17, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.905C>G (p.A302G) alteration is located in exon 8 (coding exon 8) of the COG3 gene. This alteration results from a C to G substitution at nucleotide position 905, causing the alanine (A) at amino acid position 302 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.47
BayesDel_addAF	Benign	-0.023	T
BayesDel_noAF	Benign	-0.27
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Benign	0.21	T;.
Eigen	Uncertain	0.49
Eigen_PC	Uncertain	0.57
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.94	D;D
M_CAP	Benign	0.032	D
MetaRNN	Benign	0.36	T;T
MetaSVM	Benign	-0.75	T
MutationAssessor	Uncertain	2.1	M;M
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	-2.3	N;.
REVEL	Benign	0.19
Sift	Uncertain	0.026	D;.
Sift4G	Uncertain	0.025	D;T
Polyphen		0.96	D;P
Vest4		0.41
MutPred		0.52		Gain of catalytic residue at A302 (P = 0.0032);Gain of catalytic residue at A302 (P = 0.0032);
MVP		0.35
MPC		0.44
ClinPred		0.88	D
GERP RS		5.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.26
gMVP		0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr13-46060691;