dbSNP rs143773937: COG5:p.Pro346Leu (chr7-107324511-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_006348.5(COG5):c.1037C>T(p.Pro346Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000566 in 1,602,608 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P346P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00063 ( 2 hom., cov: 33)

Exomes 𝑓: 0.00056 ( 1 hom. )

Consequence

COG5
NM_006348.5 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2B:3

Conservation

PhyloP100: 5.24

Publications

5 publications found

Variant links:

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]

COG5 Gene-Disease associations (from GenCC):

COG5-congenital disorder of glycosylation
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, G2P, Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), Orphanet

COG5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005508989).

BP6

Variant 7-107324511-G-A is Benign according to our data. Variant chr7-107324511-G-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 286064.

BS1

Variant frequency is greater than expected in population mid. GnomAdExome4 allele frequency = 0.000559 (811/1450536) while in subpopulation MID AF = 0.00175 (10/5720). AF 95% confidence interval is 0.000948. There are 1 homozygotes in GnomAdExome4. There are 424 alleles in the male GnomAdExome4 subpopulation. Median coverage is 28. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006348.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
COG5	NM_006348.5	MANE Select	c.1037C>T	p.Pro346Leu	missense	Exon 11 of 22	NP_006339.4
COG5	NM_181733.4		c.1037C>T	p.Pro346Leu	missense	Exon 11 of 21	NP_859422.3	A0AAA9X096
COG5	NM_001161520.2		c.1037C>T	p.Pro346Leu	missense	Exon 11 of 21	NP_001154992.2	A0AAA9X2X8

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
COG5	ENST00000297135.9	TSL:1 MANE Select	c.1037C>T	p.Pro346Leu	missense	Exon 11 of 22	ENSP00000297135.4	Q9UP83-4
COG5	ENST00000347053.8	TSL:1	c.1037C>T	p.Pro346Leu	missense	Exon 11 of 21	ENSP00000334703.3	A0AAA9X096
COG5	ENST00000393603.7	TSL:1	c.1037C>T	p.Pro346Leu	missense	Exon 11 of 21	ENSP00000377228.3	A0AAA9X2X8

Frequencies

GnomAD3 genomes

AF:

0.000632

AC:

AN:

151954

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000580

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000458

Gnomad ASJ

AF:

0.0101

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000412

Gnomad OTH

AF:

0.000479

GnomAD2 exomes

AF:

0.000890

AC:

222

AN:

249428

AF XY:

0.000926

show subpopulations

Gnomad AFR exome

AF:

0.000808

Gnomad AMR exome

AF:

0.000848

Gnomad ASJ exome

AF:

0.0103

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000549

Gnomad OTH exome

AF:

0.00181

GnomAD4 exome

AF:

0.000559

AC:

811

AN:

1450536

Hom.:

Cov.:

AF XY:

0.000588

AC XY:

424

AN XY:

721216

show subpopulations

African (AFR)

AF:

0.000390

AC:

AN:

33306

American (AMR)

AF:

0.000743

AC:

AN:

44426

Ashkenazi Jewish (ASJ)

AF:

0.0113

AC:

294

AN:

25922

East Asian (EAS)

AF:

0.0000762

AC:

AN:

39368

South Asian (SAS)

AF:

0.000156

AC:

AN:

83360

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52978

Middle Eastern (MID)

AF:

0.00175

AC:

AN:

5720

European-Non Finnish (NFE)

AF:

0.000327

AC:

362

AN:

1105558

Other (OTH)

AF:

0.00139

AC:

AN:

59898

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

109

146

182

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000631

AC:

AN:

152072

Hom.:

Cov.:

AF XY:

0.000605

AC XY:

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.000578

AC:

AN:

41506

American (AMR)

AF:

0.000458

AC:

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0101

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5178

South Asian (SAS)

AF:

0.00

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10530

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000412

AC:

AN:

67974

Other (OTH)

AF:

0.000474

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00141

Hom.:

Bravo

AF:

0.000816

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.000932

AC:

ExAC

AF:

0.000873

AC:

106

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

COG5-congenital disorder of glycosylation (2)

COG5-related disorder (1)

Inborn genetic diseases (1)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.36

BayesDel_noAF

Benign

-0.37

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.11

Eigen

Benign

0.13

Eigen_PC

Uncertain

0.26

FATHMM_MKL

Uncertain

0.90

LIST_S2

Uncertain

0.91

M_CAP

Benign

0.025

MetaRNN

Benign

0.0055

MetaSVM

Benign

-0.84

MutationAssessor

Uncertain

2.2

PhyloP100

5.2

PrimateAI

Benign

0.29

PROVEAN

Uncertain

-3.7

REVEL

Benign

0.087

Sift

Uncertain

0.029

Sift4G

Benign

0.061

Polyphen

0.10

Vest4

0.20

MVP

0.57

MPC

0.064

ClinPred

0.043

GERP RS

4.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.23

gMVP

0.28

Mutation Taster

=94/6

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over