rs2943134

Positions:

• chr15-28709310-C-G

Variant summary

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

The NM_001282468.3(GOLGA8M):​c.266G>C​(p.Arg89Thr) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 20)
  • Exomes 𝑓: 0.000029 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA8M NM_001282468.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.80

Genes affected

GOLGA8M (HGNC:44404): (golgin A8 family member M) 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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.11229399).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA8M	NM_001282468.3	c.266G>C	p.Arg89Thr	missense_variant	4/19	ENST00000563027.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA8M	ENST00000563027.2	c.266G>C	p.Arg89Thr	missense_variant	4/19	5	NM_001282468.3	P1
GOLGA8M	ENST00000563213.1	n.521G>C		non_coding_transcript_exon_variant	6/6	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 3 AN: 151442 Hom.: 0 Cov.: 20 FAILED QC

Gnomad AFR AF: 0.0000486

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000210

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000148 AC: 1 AN: 67582 Hom.: 0 AF XY: 0.0000298 AC XY: 1 AN XY: 33568

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 SAS exome AF: 0.000161

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: 0.0000286 AC: 41 AN: 1432662 Hom.: 1 Cov.: 31 AF XY: 0.0000324 AC XY: 23 AN XY: 709990

Gnomad4 AFR exome AF: 0.000366

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000487

Gnomad4 FIN exome AF: 0.0000195

Gnomad4 NFE exome AF: 0.00000637

Gnomad4 OTH exome AF: 0.000286

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000330 AC: 5 AN: 151556 Hom.: 0 Cov.: 20 AF XY: 0.0000540 AC XY: 4 AN XY: 74016

Gnomad4 AFR AF: 0.0000970

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000210

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	14
DANN	Benign	0.15
DEOGEN2	Benign	0.011	T
FATHMM_MKL	Benign	0.61	D
LIST_S2	Benign	0.52	T
M_CAP	Benign	0.0012	T
MetaRNN	Benign	0.11	T
MutationTaster	Benign	1.0	D;N
PROVEAN	Benign	-1.8	N
Sift	Benign	0.23	T
Sift4G	Benign	0.30	T
Vest4		0.17
MVP		0.043
MPC		2.4
GERP RS		0.78
Varity_R		0.049
gMVP		0.15

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: rs2943134; hg19: chr15-28954456;