15-34381781-G-A

Position:

• chr15-34381781-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_181077.5(GOLGA8A):​c.1529C>T​(p.Ala510Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 12)
  • Exomes 𝑓: 0.000047 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA8A NM_181077.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.617

Genes affected

GOLGA8A (HGNC:31972): (golgin A8 family member A) The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked, flattened membrane sacs referred to as cisternae. Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. The golgins constitute a family of proteins which are localized to the Golgi. This gene encodes a golgin which structurally resembles its family member GOLGA2, suggesting that they may share a similar function. There are many similar copies of this gene on chromosome 15. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.07605466).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA8A	NM_181077.5	c.1529C>T	p.Ala510Val	missense_variant	24/25	ENST00000359187.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA8A	ENST00000359187.5	c.1529C>T	p.Ala510Val	missense_variant	24/25	1	NM_181077.5	P4
GOLGA8A	ENST00000473125.5	n.3607C>T		non_coding_transcript_exon_variant	22/23	1
GOLGA8A	ENST00000699472.1	c.1526C>T	p.Ala509Val	missense_variant	24/25			A2

Frequencies

GnomAD3 genomes Cov.: 12

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000471 AC: 40 AN: 850088 Hom.: 0 Cov.: 12 AF XY: 0.0000465 AC XY: 20 AN XY: 430548

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000327

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000634

Gnomad4 OTH exome AF: 0.0000250

GnomAD4 genome Cov.: 12

Alfa AF: 0.0000843 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	16
DANN	Benign	0.68
DEOGEN2	Benign	0.032	T;.
Eigen	Benign	-0.85
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.037	N
LIST_S2	Benign	0.62	T;T
M_CAP	Benign	0.0019	T
MetaRNN	Benign	0.076	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.8	L;.
MutationTaster	Benign	1.0	N;N;N;N
PrimateAI	Uncertain	0.59	T
REVEL	Benign	0.10
Sift4G	Benign	0.076	T;T
Polyphen		0.51	P;D
Vest4		0.18
MutPred		0.25		Gain of helix (P = 0.132);.;
MVP		0.068
ClinPred		0.069	T
GERP RS		-0.71
Varity_R		0.022
gMVP		0.11

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

LitVar

Other links and lift over

dbSNP: rs1197034679; hg19: chr15-34673982;