Variant 15-30613869-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001282490.2(GOLGA8H):c.1468C>T(p.Gln490*) variant causes a stop gained, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00457 in 1,604,634 control chromosomes in the GnomAD database, including 167 homozygotes. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0028 ( 4 hom., cov: 21)

Exomes 𝑓: 0.0048 ( 163 hom. )

Consequence

GOLGA8H
NM_001282490.2 stop_gained, splice_region

Scores

Splicing: ADA: 0.007790

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0590

Variant links:

Genes affected

GOLGA8H (HGNC:37443): (golgin A8 family member H) 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]

GOLGA8H links:

ARHGAP11B-DT (HGNC:):

ARHGAP11B-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 15-30613869-C-T is Benign according to our data. Variant chr15-30613869-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2645108.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GOLGA8H	NM_001282490.2 linkuse as main transcript	c.1468C>T	p.Gln490*	stop_gained, splice_region_variant	16/19	ENST00000566740.2	NP_001269419.1	P0CJ92

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GOLGA8H	ENST00000566740.2 linkuse as main transcript	c.1468C>T	p.Gln490*	stop_gained, splice_region_variant	16/19	5	NM_001282490.2	ENSP00000456894.1		P0CJ92

Frequencies

GnomAD3 genomes

AF:

0.00280

AC:

423

AN:

151050

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00127

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00119

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000835

Gnomad FIN

AF:

0.0000951

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00505

Gnomad OTH

AF:

0.00290

GnomAD3 exomes

AF:

0.00247

AC:

592

AN:

239268

Hom.:

AF XY:

0.00256

AC XY:

335

AN XY:

130840

show subpopulations

Gnomad AFR exome

AF:

0.00112

Gnomad AMR exome

AF:

0.00131

Gnomad ASJ exome

AF:

0.000101

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00177

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00421

Gnomad OTH exome

AF:

0.00185

GnomAD4 exome

AF:

0.00475

AC:

6911

AN:

1453466

Hom.:

163

Cov.:

AF XY:

0.00469

AC XY:

3393

AN XY:

723316

show subpopulations

Gnomad4 AFR exome

AF:

0.000718

Gnomad4 AMR exome

AF:

0.00114

Gnomad4 ASJ exome

AF:

0.000153

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00183

Gnomad4 FIN exome

AF:

0.000172

Gnomad4 NFE exome

AF:

0.00571

Gnomad4 OTH exome

AF:

0.00527

GnomAD4 genome

AF:

0.00280

AC:

423

AN:

151168

Hom.:

Cov.:

AF XY:

0.00234

AC XY:

173

AN XY:

73926

show subpopulations

Gnomad4 AFR

AF:

0.00126

Gnomad4 AMR

AF:

0.00119

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000836

Gnomad4 FIN

AF:

0.0000951

Gnomad4 NFE

AF:

0.00505

Gnomad4 OTH

AF:

0.00287

Alfa

AF:

0.00309

Hom.:

Bravo

AF:

0.00276

ExAC

AF:

0.00219

AC:

259

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

Feb 01, 2023

GOLGA8H: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.12

BayesDel_noAF

Pathogenic

0.39

CADD

Pathogenic

DANN

Benign

0.95

FATHMM_MKL

Benign

0.068

Vest4

0.022

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0078

dbscSNV1_RF

Benign

0.28

SpliceAI score (max)

0.030

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