15-28385324-A-G

Variant names:

• chr15-28385324-A-G
• rs2044268
• NM_001350920.2:c.1077A>G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001350920.2(GOLGA8F):​c.1077A>G​(p.Pro359Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00255 in 144,508 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0025 (0 hom., cov: 21)
  • Exomes 𝑓: 0.0014 (2 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA8F NM_001350920.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.16

Genes affected

GOLGA8F (HGNC:32378): (golgin A8 family member F) 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 Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP6: Variant 15-28385324-A-G is Benign according to our data. Variant chr15-28385324-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2645089.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=1.16 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA8F	NM_001350920.2	c.1077A>G	p.Pro359Pro	synonymous_variant	Exon 12 of 19	ENST00000526619.7	NP_001337849.2
GOLGA8F	NR_033351.2	n.1474A>G		non_coding_transcript_exon_variant	Exon 11 of 18
GOLGA8F	XR_002957623.2	n.1201A>G		non_coding_transcript_exon_variant	Exon 12 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8F	ENST00000526619.7	c.1077A>G	p.Pro359Pro	synonymous_variant	Exon 12 of 19	1	NM_001350920.2	ENSP00000456138.3
GOLGA8F	ENST00000532622.8	n.1448A>G		non_coding_transcript_exon_variant	Exon 11 of 18	5

Frequencies

GnomAD3 genomes AF: 0.00255 AC: 369 AN: 144434 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.00128

Gnomad AMI AF: 0.00228

Gnomad AMR AF: 0.00699

Gnomad ASJ AF: 0.00614

Gnomad EAS AF: 0.000198

Gnomad SAS AF: 0.00776

Gnomad FIN AF: 0.000765

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00234

Gnomad OTH AF: 0.00205

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00137 AC: 847 AN: 618382 Hom.: 2 Cov.: 6 AF XY: 0.00153 AC XY: 513 AN XY: 334764

Gnomad4 AFR exome AF: 0.000845

Gnomad4 AMR exome AF: 0.00298

Gnomad4 ASJ exome AF: 0.00136

Gnomad4 EAS exome AF: 0.000110

Gnomad4 SAS exome AF: 0.00534

Gnomad4 FIN exome AF: 0.000439

Gnomad4 NFE exome AF: 0.000742

Gnomad4 OTH exome AF: 0.00126

GnomAD4 genome AF: 0.00255 AC: 368 AN: 144508 Hom.: 0 Cov.: 21 AF XY: 0.00273 AC XY: 192 AN XY: 70426

Gnomad4 AFR AF: 0.00128

Gnomad4 AMR AF: 0.00699

Gnomad4 ASJ AF: 0.00614

Gnomad4 EAS AF: 0.000199

Gnomad4 SAS AF: 0.00755

Gnomad4 FIN AF: 0.000765

Gnomad4 NFE AF: 0.00235

Gnomad4 OTH AF: 0.00204

Alfa AF: 0.00300 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Mar 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

GOLGA8F: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.52
DANN	Benign	0.41

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: rs2044268; hg19: chr15-28630470;