Genetic Variant NM_001023567.5:c.325-9T>C (chr15-34531704-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

0 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 774220.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001023567.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA8B	NM_001023567.5	MANE Select	c.325-9T>C		intron	N/A	NP_001018861.3	A8MQT2-1
	GOLGA8B	NR_027410.2		n.2763-9T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GOLGA8B	ENST00000683415.1	MANE Select	c.325-9T>C	intron	N/A	ENSP00000507830.1	A8MQT2-1
GOLGA8B	ENST00000342314.9	TSL:1	c.325-9T>C	intron	N/A	ENSP00000343064.5	A8MQT2-1
GOLGA8B	ENST00000484716.5	TSL:1	n.2649-9T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0178

AC:

1553

AN:

87352

Hom.:

216

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.0240

AC:

1228

AN:

51098

AF XY:

0.0228

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 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

African (AFR)

AF:

0.00645

AC:

AN:

13640

American (AMR)

AF:

0.0174

AC:

348

AN:

19964

Ashkenazi Jewish (ASJ)

AF:

0.0570

AC:

847

AN:

14858

East Asian (EAS)

AF:

0.000362

AC:

AN:

16564

South Asian (SAS)

AF:

0.0124

AC:

510

AN:

40970

European-Finnish (FIN)

AF:

0.00372

AC:

AN:

24968

Middle Eastern (MID)

AF:

0.0496

AC:

AN:

1674

European-Non Finnish (NFE)

AF:

0.0369

AC:

8360

AN:

226856

Other (OTH)

AF:

0.0305

AC:

668

AN:

21888

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

212

424

635

847

1059

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

African (AFR)

AF:

0.00473

AC:

149

AN:

31526

American (AMR)

AF:

0.0189

AC:

152

AN:

8042

Ashkenazi Jewish (ASJ)

AF:

0.0580

AC:

131

AN:

2258

East Asian (EAS)

AF:

0.00

AC:

AN:

1518

South Asian (SAS)

AF:

0.00587

AC:

AN:

1704

European-Finnish (FIN)

AF:

0.00211

AC:

AN:

4732

Middle Eastern (MID)

AF:

0.0423

AC:

AN:

142

European-Non Finnish (NFE)

AF:

0.0297

AC:

1068

AN:

35956

Other (OTH)

AF:

0.0152

AC:

AN:

1120

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

133

177

221

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0214

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

3.0

(source)

DANN

Benign

0.25

PhyloP100

0.10

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over