Variant 15-28702692-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001282468.3(GOLGA8M):c.1422G>A(p.Lys474=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00235 in 1,601,050 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 2 hom., cov: 29)

Exomes 𝑓: 0.0023 ( 48 hom. )

Consequence

GOLGA8M
NM_001282468.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0990

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 -11 ACMG points.

BP4

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

BP6

Variant 15-28702692-C-T is Benign according to our data. Variant chr15-28702692-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2645091.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.099 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA8M	NM_001282468.3 linkuse as main transcript	c.1422G>A	p.Lys474=	synonymous_variant	16/19	ENST00000563027.2
LOC107984746	XR_001751465.2 linkuse as main transcript	n.90-36C>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.1422G>A	p.Lys474=	synonymous_variant	16/19	5	NM_001282468.3	P1	H3BSY2-1

Frequencies

GnomAD3 genomes

AF:

0.00320

AC:

485

AN:

151468

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00289

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.00342

Gnomad ASJ

AF:

0.00808

Gnomad EAS

AF:

0.00695

Gnomad SAS

AF:

0.00711

Gnomad FIN

AF:

0.00123

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00272

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.00273

AC:

659

AN:

241124

Hom.:

AF XY:

0.00299

AC XY:

393

AN XY:

131364

show subpopulations

Gnomad AFR exome

AF:

0.00180

Gnomad AMR exome

AF:

0.00289

Gnomad ASJ exome

AF:

0.00457

Gnomad EAS exome

AF:

0.00506

Gnomad SAS exome

AF:

0.00592

Gnomad FIN exome

AF:

0.000433

Gnomad NFE exome

AF:

0.00174

Gnomad OTH exome

AF:

0.00267

GnomAD4 exome

AF:

0.00226

AC:

3281

AN:

1449474

Hom.:

Cov.:

AF XY:

0.00252

AC XY:

1818

AN XY:

721382

show subpopulations

Gnomad4 AFR exome

AF:

0.00181

Gnomad4 AMR exome

AF:

0.00352

Gnomad4 ASJ exome

AF:

0.00801

Gnomad4 EAS exome

AF:

0.00393

Gnomad4 SAS exome

AF:

0.00765

Gnomad4 FIN exome

AF:

0.00106

Gnomad4 NFE exome

AF:

0.00160

Gnomad4 OTH exome

AF:

0.00298

GnomAD4 genome

AF:

0.00319

AC:

484

AN:

151576

Hom.:

Cov.:

AF XY:

0.00324

AC XY:

240

AN XY:

74058

show subpopulations

Gnomad4 AFR

AF:

0.00288

Gnomad4 AMR

AF:

0.00342

Gnomad4 ASJ

AF:

0.00808

Gnomad4 EAS

AF:

0.00677

Gnomad4 SAS

AF:

0.00711

Gnomad4 FIN

AF:

0.00123

Gnomad4 NFE

AF:

0.00272

Gnomad4 OTH

AF:

0.00522

Alfa

AF:

0.00470

Hom.:

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

Mar 01, 2023

GOLGA8M: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

0.91

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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