Genetic Variant GOLGA8O:p.Glu437Glu (chr15-32446531-C-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001277308.1(GOLGA8O):c.1311G>A(p.Glu437Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00042 ( 0 hom., cov: 19)

Exomes 𝑓: 0.00029 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA8O
NM_001277308.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.354

Variant links:

Genes affected

GOLGA8O (HGNC:44406): (golgin A8 family member O) Predicted to be involved in Golgi organization. Predicted to be located in Golgi apparatus. Predicted to be active in Golgi cis cisterna; Golgi cisterna membrane; and cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

GOLGA8O links:

RN7SL539P (HGNC:46555): (RNA, 7SL, cytoplasmic 539, pseudogene)

RN7SL539P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 15-32446531-C-T is Benign according to our data. Variant chr15-32446531-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2645125.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.354 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA8O	NM_001277308.1 link	c.1311G>A	p.Glu437Glu	synonymous_variant	Exon 15 of 19	ENST00000509311.7	NP_001264237.1	A6NCC3-2
GOLGA8O	XM_047433006.1 link	c.1272G>A	p.Glu424Glu	synonymous_variant	Exon 15 of 19		XP_047288962.1
GOLGA8O	XM_011521988.4 link	c.1242G>A	p.Glu414Glu	synonymous_variant	Exon 14 of 18		XP_011520290.1
GOLGA8O	XM_024450042.2 link	c.858G>A	p.Glu286Glu	synonymous_variant	Exon 15 of 19		XP_024305810.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8O	ENST00000509311.7 link	c.1311G>A	p.Glu437Glu	synonymous_variant	Exon 15 of 19	5	NM_001277308.1	ENSP00000423159.2		A6NCC3-2
RN7SL539P	ENST00000610974.1 link	n.*143G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

129798

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0000843

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000417

Gnomad ASJ

AF:

0.00255

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000590

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000540

Gnomad OTH

AF:

0.00171

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000292

AC:

422

AN:

1446992

Hom.:

Cov.:

AF XY:

0.000363

AC XY:

261

AN XY:

719596

show subpopulations

Gnomad4 AFR exome

AF:

0.0000601

Gnomad4 AMR exome

AF:

0.000320

Gnomad4 ASJ exome

AF:

0.000703

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000232

Gnomad4 OTH exome

AF:

0.000437

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000416

AC:

AN:

129914

Hom.:

Cov.:

AF XY:

0.000428

AC XY:

AN XY:

63104

show subpopulations

Gnomad4 AFR

AF:

0.0000841

Gnomad4 AMR

AF:

0.000417

Gnomad4 ASJ

AF:

0.00255

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000592

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000540

Gnomad4 OTH

AF:

0.00169

Alfa

AF:

0.00182

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

GOLGA8O: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

5.4

DANN

Benign

0.72

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over