rs773449359

Variant names:

• chr7-107210554-A-C
• NM_006348.5:c.2347T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-107210554-A-C
• chr7-107210554-A-G
• chr7-107210554-A-T

Variant summary

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

The NM_006348.5(COG5):​c.2347T>G​(p.Ser783Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000000689 in 1,451,268 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: COG5 NM_006348.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.79

Genes affected

COG5 (HGNC:14857): (component of oligomeric golgi complex 5) The protein encoded by this gene is one of eight proteins (Cog1-8) which form a Golgi-localized complex (COG) required for normal Golgi morphology and function. The encoded protein is organized with conserved oligomeric Golgi complex components 6, 7 and 8 into a sub-complex referred to as lobe B. Alternative splicing results in multiple transcript variants. Mutations in this gene result in congenital disorder of glycosylation type 2I.[provided by RefSeq, Jan 2011]

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=0.15770146).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COG5	NM_006348.5	c.2347T>G	p.Ser783Ala	missense_variant	Exon 21 of 22	ENST00000297135.9	NP_006339.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COG5	ENST00000297135.9	c.2347T>G	p.Ser783Ala	missense_variant	Exon 21 of 22	1	NM_006348.5	ENSP00000297135.4
COG5	ENST00000347053.8	c.2284T>G	p.Ser762Ala	missense_variant	Exon 20 of 21	1		ENSP00000334703.3
COG5	ENST00000393603.7	c.2347T>G	p.Ser783Ala	missense_variant	Exon 21 of 21	1		ENSP00000377228.3
COG5	ENST00000464542.5	n.798T>G		non_coding_transcript_exon_variant	Exon 6 of 6	3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.89e-7 AC: 1 AN: 1451268 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 720518

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000190

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.066
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.011	T;.;.
Eigen	Benign	-0.055
Eigen_PC	Benign	0.072
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.68	T;T;T
M_CAP	Benign	0.0068	T
MetaRNN	Benign	0.16	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.1	M;.;.
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-1.9	N;N;N
REVEL	Benign	0.063
Sift	Uncertain	0.021	D;D;D
Sift4G	Benign	0.074	T;T;T
Polyphen		0.0090	B;B;.
Vest4		0.31
MutPred		0.20		Loss of disorder (P = 0.0649);.;.;
MVP		0.42
MPC		0.050
ClinPred		0.97	D
GERP RS		4.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.28
gMVP		0.25

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-106850999;