rs12535761

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000297135.9(COG5):​c.538+28407T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,200 control chromosomes in the GnomAD database, including 1,503 homozygotes. 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: 𝑓 0.13 ( 1503 hom., cov: 32)

Consequence

COG5
ENST00000297135.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0990
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COG5NM_006348.5 linkuse as main transcriptc.538+28407T>G intron_variant ENST00000297135.9 NP_006339.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COG5ENST00000297135.9 linkuse as main transcriptc.538+28407T>G intron_variant 1 NM_006348.5 ENSP00000297135 P2
COG5ENST00000347053.8 linkuse as main transcriptc.538+28407T>G intron_variant 1 ENSP00000334703 A2
COG5ENST00000393603.7 linkuse as main transcriptc.538+28407T>G intron_variant 1 ENSP00000377228
COG5ENST00000475638.6 linkuse as main transcriptn.295+28407T>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.126
AC:
19105
AN:
152082
Hom.:
1505
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0335
Gnomad AMI
AF:
0.224
Gnomad AMR
AF:
0.132
Gnomad ASJ
AF:
0.157
Gnomad EAS
AF:
0.135
Gnomad SAS
AF:
0.135
Gnomad FIN
AF:
0.154
Gnomad MID
AF:
0.117
Gnomad NFE
AF:
0.172
Gnomad OTH
AF:
0.127
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.125
AC:
19099
AN:
152200
Hom.:
1503
Cov.:
32
AF XY:
0.124
AC XY:
9250
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.0334
Gnomad4 AMR
AF:
0.132
Gnomad4 ASJ
AF:
0.157
Gnomad4 EAS
AF:
0.135
Gnomad4 SAS
AF:
0.135
Gnomad4 FIN
AF:
0.154
Gnomad4 NFE
AF:
0.172
Gnomad4 OTH
AF:
0.126
Alfa
AF:
0.0453
Hom.:
57
Bravo
AF:
0.123

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
7.5
DANN
Benign
0.65

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12535761; hg19: chr7-107139275; API