Variant 15-28703925-G-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.1201-8C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00329 in 1,589,170 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts 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 0.0026 ( 3 hom., cov: 28)

Exomes 𝑓: 0.0034 ( 22 hom. )

Consequence

GOLGA8M
NM_001282468.3 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.006166

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0280

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 (BayesDel_noAF=-0.69).

BP6

Variant 15-28703925-G-T is Benign according to our data. Variant chr15-28703925-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2645092.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA8M	NM_001282468.3 linkuse as main transcript	c.1201-8C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000563027.2
LOC107984746	XR_001751465.2 linkuse as main transcript	n.186+1101G>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.1201-8C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_001282468.3	P1	H3BSY2-1

Frequencies

GnomAD3 genomes

AF:

0.00263

AC:

393

AN:

149464

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000495

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000679

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00466

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00458

Gnomad OTH

AF:

0.00146

GnomAD3 exomes

AF:

0.00226

AC:

313

AN:

138204

Hom.:

AF XY:

0.00195

AC XY:

145

AN XY:

74494

show subpopulations

Gnomad AFR exome

AF:

0.000807

Gnomad AMR exome

AF:

0.000390

Gnomad ASJ exome

AF:

0.000122

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00265

Gnomad NFE exome

AF:

0.00442

Gnomad OTH exome

AF:

0.00308

GnomAD4 exome

AF:

0.00336

AC:

4831

AN:

1439588

Hom.:

Cov.:

AF XY:

0.00321

AC XY:

2299

AN XY:

716490

show subpopulations

Gnomad4 AFR exome

AF:

0.000669

Gnomad4 AMR exome

AF:

0.000491

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000267

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00436

Gnomad4 NFE exome

AF:

0.00400

Gnomad4 OTH exome

AF:

0.00264

GnomAD4 genome

AF:

0.00263

AC:

393

AN:

149582

Hom.:

Cov.:

AF XY:

0.00245

AC XY:

179

AN XY:

72964

show subpopulations

Gnomad4 AFR

AF:

0.000494

Gnomad4 AMR

AF:

0.000678

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00466

Gnomad4 NFE

AF:

0.00458

Gnomad4 OTH

AF:

0.00144

Alfa

AF:

0.00144

Hom.:

Bravo

AF:

0.00209

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

Aug 01, 2023

GOLGA8M: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

5.2

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0062

dbscSNV1_RF

Benign

0.15

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