Genetic Variant GOLGA8B:c.325-9T>C (chr15-34531704-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001023567.5(GOLGA8B):c.325-9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 216 hom., cov: 12)

Exomes 𝑓: 0.029 ( 3057 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA8B
NM_001023567.5 intron

Scores

Splicing: ADA: 0.00002340

Clinical Significance

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

Conservation

PhyloP100: 0.105

Variant links:

Genes affected

GOLGA8B (HGNC:31973): (golgin A8 family member B) Predicted to be involved in Golgi organization and spindle assembly. Located in Golgi apparatus and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

GOLGA8B 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 (BayesDel_noAF=-0.94).

BP6

Variant 15-34531704-A-G is Benign according to our data. Variant chr15-34531704-A-G is described in ClinVar as [Benign]. Clinvar id is 774220.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA8B	NM_001023567.5 link	c.325-9T>C		intron_variant	Intron 12 of 23	ENST00000683415.1	NP_001018861.3	A8MQT2-1
GOLGA8B	NR_027410.2 link	n.2763-9T>C		intron_variant	Intron 12 of 23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8B	ENST00000683415.1 link	c.325-9T>C		intron_variant	Intron 12 of 23		NM_001023567.5	ENSP00000507830.1		A8MQT2-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

1553

AN:

87352

Hom.:

216

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00474

Gnomad AMI

AF:

0.0248

Gnomad AMR

AF:

0.0189

Gnomad ASJ

AF:

0.0580

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00529

Gnomad FIN

AF:

0.00211

Gnomad MID

AF:

0.0417

Gnomad NFE

AF:

0.0297

Gnomad OTH

AF:

0.0153

GnomAD3 exomes

AF:

0.0240

AC:

1228

AN:

51098

Hom.:

324

AF XY:

0.0228

AC XY:

589

AN XY:

25852

show subpopulations

Gnomad AFR exome

AF:

0.00537

Gnomad AMR exome

AF:

0.0169

Gnomad ASJ exome

AF:

0.0497

Gnomad EAS exome

AF:

0.000443

Gnomad SAS exome

AF:

0.0112

Gnomad FIN exome

AF:

0.00352

Gnomad NFE exome

AF:

0.0392

Gnomad OTH exome

AF:

0.0240

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0289

AC:

11003

AN:

381382

Hom.:

3057

Cov.:

AF XY:

0.0284

AC XY:

5825

AN XY:

205432

show subpopulations

Gnomad4 AFR exome

AF:

0.00645

Gnomad4 AMR exome

AF:

0.0174

Gnomad4 ASJ exome

AF:

0.0570

Gnomad4 EAS exome

AF:

0.000362

Gnomad4 SAS exome

AF:

0.0124

Gnomad4 FIN exome

AF:

0.00372

Gnomad4 NFE exome

AF:

0.0369

Gnomad4 OTH exome

AF:

0.0305

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0178

AC:

1554

AN:

87442

Hom.:

216

Cov.:

AF XY:

0.0168

AC XY:

697

AN XY:

41424

show subpopulations

Gnomad4 AFR

AF:

0.00473

Gnomad4 AMR

AF:

0.0189

Gnomad4 ASJ

AF:

0.0580

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00587

Gnomad4 FIN

AF:

0.00211

Gnomad4 NFE

AF:

0.0297

Gnomad4 OTH

AF:

0.0152

Alfa

AF:

0.0214

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Dec 13, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

3.0

DANN

Benign

0.25

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000023

dbscSNV1_RF

Benign

0.0020

SpliceAI score (max)

0.010

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