dbSNP rs1442309623: GOLGA8B:p.Gly504Glu (chr15-34528020-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001023567.5(GOLGA8B):c.1511G>A(p.Gly504Glu) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 8)

Exomes 𝑓: 0.0000089 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA8B
NM_001023567.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.53

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: Likely_benign. The variant received -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.19912097).

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.1511G>A	p.Gly504Glu	missense	Exon 23 of 24	NP_001018861.3	A8MQT2-1
	GOLGA8B	NR_027410.2		n.3949G>A		non_coding_transcript_exon	Exon 23 of 24

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GOLGA8B	ENST00000683415.1	MANE Select	c.1511G>A	p.Gly504Glu	missense	Exon 23 of 24	ENSP00000507830.1	A8MQT2-1
GOLGA8B	ENST00000342314.9	TSL:1	c.1511G>A	p.Gly504Glu	missense	Exon 15 of 16	ENSP00000343064.5	A8MQT2-1
GOLGA8B	ENST00000484716.5	TSL:1	n.3835G>A		non_coding_transcript_exon	Exon 22 of 23

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.0000160

AC:

AN:

62580

AF XY:

0.0000303

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000885

AC:

AN:

790604

Hom.:

Cov.:

AF XY:

0.00000741

AC XY:

AN XY:

405034

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

14836

American (AMR)

AF:

0.00

AC:

AN:

25866

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15866

East Asian (EAS)

AF:

0.00

AC:

AN:

32176

South Asian (SAS)

AF:

0.0000166

AC:

AN:

60088

European-Finnish (FIN)

AF:

0.00

AC:

AN:

34814

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2648

European-Non Finnish (NFE)

AF:

0.0000106

AC:

AN:

567792

Other (OTH)

AF:

0.00

AC:

AN:

36518

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00000064186), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.346

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.13

BayesDel_noAF

Benign

-0.42

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.037

Eigen

Benign

-0.31

Eigen_PC

Benign

-0.49

FATHMM_MKL

Uncertain

0.79

LIST_S2

Benign

0.45

M_CAP

Benign

0.0031

MetaRNN

Benign

0.20

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.0

PhyloP100

4.5

PrimateAI

Uncertain

0.76

PROVEAN

Pathogenic

-4.8

REVEL

Benign

0.11

Sift

Benign

0.14

Sift4G

Benign

0.12

Polyphen

1.0

Vest4

0.26

MutPred

0.35

Loss of catalytic residue at G504 (P = 0.0308)

MVP

0.10

ClinPred

0.38

GERP RS

1.5

Varity_R

0.40

gMVP

0.11

Mutation Taster

=91/9

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over