Variant 15-28702369-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001282468.3(GOLGA8M):c.1568G>A(p.Gly523Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000808 in 1,380,934 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0010 ( 1 hom., cov: 22)

Exomes 𝑓: 0.00081 ( 6 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA8M
NM_001282468.3 missense, splice_region

Scores

Splicing: ADA: 0.005558

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.126

Variant links:

Genes affected

GOLGA8M (HGNC:44404): (golgin A8 family member M) Predicted to be involved in Golgi organization. Predicted to be active in Golgi cis cisterna; Golgi cisterna membrane; and cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

GOLGA8M links:

LOC107984746 (HGNC:):

LOC107984746 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0071184337).

BP6

Variant 15-28702369-C-T is Benign according to our data. Variant chr15-28702369-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2645090.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA8M	NM_001282468.3 linkuse as main transcript	c.1568G>A	p.Gly523Asp	missense_variant, splice_region_variant	18/19	ENST00000563027.2
LOC107984746	XR_001751465.2 linkuse as main transcript	n.89+262C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA8M	ENST00000563027.2 linkuse as main transcript	c.1568G>A	p.Gly523Asp	missense_variant, splice_region_variant	18/19	5	NM_001282468.3	P1	H3BSY2-1

Frequencies

GnomAD3 genomes

AF:

0.00101

AC:

145

AN:

144000

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000652

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00325

Gnomad ASJ

AF:

0.00292

Gnomad EAS

AF:

0.00267

Gnomad SAS

AF:

0.00181

Gnomad FIN

AF:

0.000290

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000584

Gnomad OTH

AF:

0.00101

GnomAD3 exomes

AF:

0.00134

AC:

178

AN:

132924

Hom.:

AF XY:

0.00149

AC XY:

108

AN XY:

72336

show subpopulations

Gnomad AFR exome

AF:

0.000923

Gnomad AMR exome

AF:

0.00168

Gnomad ASJ exome

AF:

0.00285

Gnomad EAS exome

AF:

0.00231

Gnomad SAS exome

AF:

0.00144

Gnomad FIN exome

AF:

0.000353

Gnomad NFE exome

AF:

0.000727

Gnomad OTH exome

AF:

0.00318

GnomAD4 exome

AF:

0.000808

AC:

1116

AN:

1380934

Hom.:

Cov.:

AF XY:

0.000844

AC XY:

575

AN XY:

681388

show subpopulations

Gnomad4 AFR exome

AF:

0.000510

Gnomad4 AMR exome

AF:

0.00182

Gnomad4 ASJ exome

AF:

0.00398

Gnomad4 EAS exome

AF:

0.00631

Gnomad4 SAS exome

AF:

0.00150

Gnomad4 FIN exome

AF:

0.000265

Gnomad4 NFE exome

AF:

0.000476

Gnomad4 OTH exome

AF:

0.00114

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00101

AC:

145

AN:

144100

Hom.:

Cov.:

AF XY:

0.000869

AC XY:

AN XY:

70156

show subpopulations

Gnomad4 AFR

AF:

0.000650

Gnomad4 AMR

AF:

0.00324

Gnomad4 ASJ

AF:

0.00292

Gnomad4 EAS

AF:

0.00268

Gnomad4 SAS

AF:

0.00181

Gnomad4 FIN

AF:

0.000290

Gnomad4 NFE

AF:

0.000584

Gnomad4 OTH

AF:

0.00100

Alfa

AF:

0.00120

Hom.:

ExAC

AF:

0.000746

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

GOLGA8M: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.065

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.49

M_CAP

Benign

0.00040

MetaRNN

Benign

0.0071

MutationTaster

Benign

0.97

PROVEAN

Uncertain

-3.3

Sift

Benign

0.12

Sift4G

Benign

0.54

Vest4

0.33

MVP

0.18

MPC

0.64

GERP RS

-0.27

Varity_R

0.12

gMVP

0.11

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0056

dbscSNV1_RF

Benign

0.18

SpliceAI score (max)

0.040

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