Variant chr15-34381521-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_181077.5(GOLGA8A):c.1702G>A(p.Val568Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 8794 hom., cov: 32)

Exomes 𝑓: 0.54 ( 117523 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA8A
NM_181077.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.64

Variant links:

Genes affected

GOLGA8A (HGNC:31972): (golgin A8 family member A) The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked, flattened membrane sacs referred to as cisternae. Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. The golgins constitute a family of proteins which are localized to the Golgi. This gene encodes a golgin which structurally resembles its family member GOLGA2, suggesting that they may share a similar function. There are many similar copies of this gene on chromosome 15. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]

GOLGA8A links:

GOLGA8A (HGNC:):

GOLGA8A links:

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 (MetaRNN=0.0016046166).

BP6

Variant 15-34381521-C-T is Benign according to our data. Variant chr15-34381521-C-T is described in ClinVar as [Benign]. Clinvar id is 768693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GOLGA8A	NM_181077.5 linkuse as main transcript	c.1702G>A	p.Val568Ile	missense_variant	25/25	ENST00000359187.5	NP_851422.1	A7E2F4-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GOLGA8A	ENST00000359187.5 linkuse as main transcript	c.1702G>A	p.Val568Ile	missense_variant	25/25	1	NM_181077.5	ENSP00000352111.4	A7E2F4-3
GOLGA8A	ENST00000473125.5 linkuse as main transcript	n.3780G>A		non_coding_transcript_exon_variant	23/23	1
GOLGA8A	ENST00000699472.1 linkuse as main transcript	c.1699G>A	p.Val567Ile	missense_variant	25/25			ENSP00000514395.1	A0A8V8TPN8

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

65998

AN:

141330

Hom.:

8798

Cov.:

FAILED QC

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.528

Gnomad AMR

AF:

0.503

Gnomad ASJ

AF:

0.461

Gnomad EAS

AF:

0.588

Gnomad SAS

AF:

0.567

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.539

Gnomad NFE

AF:

0.544

Gnomad OTH

AF:

0.488

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.540

AC:

762344

AN:

1410578

Hom.:

117523

Cov.:

140

AF XY:

0.543

AC XY:

381254

AN XY:

702498

show subpopulations

Gnomad4 AFR exome

AF:

0.266

Gnomad4 AMR exome

AF:

0.502

Gnomad4 ASJ exome

AF:

0.471

Gnomad4 EAS exome

AF:

0.609

Gnomad4 SAS exome

AF:

0.585

Gnomad4 FIN exome

AF:

0.543

Gnomad4 NFE exome

AF:

0.546

Gnomad4 OTH exome

AF:

0.527

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.467

AC:

66015

AN:

141446

Hom.:

8794

Cov.:

AF XY:

0.470

AC XY:

32407

AN XY:

68954

show subpopulations

Gnomad4 AFR

AF:

0.276

Gnomad4 AMR

AF:

0.503

Gnomad4 ASJ

AF:

0.461

Gnomad4 EAS

AF:

0.589

Gnomad4 SAS

AF:

0.566

Gnomad4 FIN

AF:

0.539

Gnomad4 NFE

AF:

0.544

Gnomad4 OTH

AF:

0.484

Alfa

AF:

0.463

Hom.:

1059

ExAC

AF:

0.526

AC:

63905

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.065

BayesDel_addAF

Benign

-0.79

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.29

DANN

Benign

0.71

DEOGEN2

Benign

0.011

T;.

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.00075

LIST_S2

Benign

0.39

T;T

MetaRNN

Benign

0.0016

T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

-2.7

N;.

PrimateAI

Uncertain

0.62

PROVEAN

Benign

0.72

.;N

REVEL

Benign

0.053

Sift

Benign

1.0

.;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.019

ClinPred

0.0040

GERP RS

0.51

Varity_R

0.042

gMVP

0.089

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