chr15-28706648-G-T

Position:

• chr15-28706648-G-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001282468.3(GOLGA8M):​c.643C>A​(p.Arg215=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00401 in 1,541,804 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0031 (0 hom., cov: 27)
  • Exomes 𝑓: 0.0041 (24 hom.)
• Consequence: GOLGA8M NM_001282468.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.329

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]

LOC107984746 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 15-28706648-G-T is Benign according to our data. Variant chr15-28706648-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3025293.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 24 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA8M	NM_001282468.3	c.643C>A	p.Arg215=	synonymous_variant	9/19	ENST00000563027.2
LOC107984746	XR_001751465.2	n.1599G>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA8M	ENST00000563027.2	c.643C>A	p.Arg215=	synonymous_variant	9/19	5	NM_001282468.3	P1

Frequencies

GnomAD3 genomes AF: 0.00306 AC: 459 AN: 150192 Hom.: 0 Cov.: 27

Gnomad AFR AF: 0.000540

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00162

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00169

Gnomad FIN AF: 0.00514

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00502

Gnomad OTH AF: 0.00146

GnomAD3 exomes AF: 0.00391 AC: 335 AN: 85586 Hom.: 29 AF XY: 0.00375 AC XY: 168 AN XY: 44802

Gnomad AFR exome AF: 0.000527

Gnomad AMR exome AF: 0.00440

Gnomad ASJ exome AF: 0.00119

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00258

Gnomad FIN exome AF: 0.00567

Gnomad NFE exome AF: 0.00497

Gnomad OTH exome AF: 0.00302

GnomAD4 exome AF: 0.00411 AC: 5718 AN: 1391492 Hom.: 24 Cov.: 25 AF XY: 0.00410 AC XY: 2850 AN XY: 694660

Gnomad4 AFR exome AF: 0.000867

Gnomad4 AMR exome AF: 0.00251

Gnomad4 ASJ exome AF: 0.00117

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00278

Gnomad4 FIN exome AF: 0.00569

Gnomad4 NFE exome AF: 0.00455

Gnomad4 OTH exome AF: 0.00342

GnomAD4 genome AF: 0.00305 AC: 459 AN: 150312 Hom.: 0 Cov.: 27 AF XY: 0.00275 AC XY: 202 AN XY: 73336

Gnomad4 AFR AF: 0.000538

Gnomad4 AMR AF: 0.00162

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00170

Gnomad4 FIN AF: 0.00514

Gnomad4 NFE AF: 0.00502

Gnomad4 OTH AF: 0.00144

Alfa AF: 0.00243 Hom.: 5

Bravo AF: 0.00283

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2023

GOLGA8M: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.21		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.21		Position offset: -35

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs199923814; hg19: chr15-28951794;