15-28387606-T-C

Variant names:

• chr15-28387606-T-C
• rs749508373
• NM_001350920.2:c.1284T>C

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.1284T>C​(p.Asp428Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00072 (0 hom., cov: 19)
  • Exomes 𝑓: 0.0011 (15 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA8F NM_001350920.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.25

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]

RN7SL238P (HGNC:46254): (RNA, 7SL, cytoplasmic 238, pseudogene)

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 15-28387606-T-C is Benign according to our data. Variant chr15-28387606-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3770810.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.25 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA8F	NM_001350920.2	c.1284T>C	p.Asp428Asp	synonymous_variant	Exon 15 of 19	ENST00000526619.7	NP_001337849.2
GOLGA8F	NR_033351.2	n.1681T>C		non_coding_transcript_exon_variant	Exon 14 of 18
GOLGA8F	XR_002957623.2	n.1403+442T>C		intron_variant	Intron 14 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8F	ENST00000526619.7	c.1284T>C	p.Asp428Asp	synonymous_variant	Exon 15 of 19	1	NM_001350920.2	ENSP00000456138.3
GOLGA8F	ENST00000532622.8	n.1655T>C		non_coding_transcript_exon_variant	Exon 14 of 18	5
RN7SL238P	ENST00000613832.1	n.*121T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 100 AN: 137964 Hom.: 0 Cov.: 19 FAILED QC

Gnomad AFR AF: 0.00138

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000211

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00180

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.000191

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000351

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000746 AC: 148 AN: 198386 Hom.: 2 AF XY: 0.000860 AC XY: 92 AN XY: 107004

Gnomad AFR exome AF: 0.000921

Gnomad AMR exome AF: 0.000144

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000988

Gnomad SAS exome AF: 0.00448

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000177

Gnomad OTH exome AF: 0.000611

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00110 AC: 841 AN: 767918 Hom.: 15 Cov.: 11 AF XY: 0.00134 AC XY: 548 AN XY: 408412

Gnomad4 AFR exome AF: 0.00203

Gnomad4 AMR exome AF: 0.000438

Gnomad4 ASJ exome AF: 0.0000942

Gnomad4 EAS exome AF: 0.00218

Gnomad4 SAS exome AF: 0.00613

Gnomad4 FIN exome AF: 0.0000753

Gnomad4 NFE exome AF: 0.000462

Gnomad4 OTH exome AF: 0.000966

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000724 AC: 100 AN: 138044 Hom.: 0 Cov.: 19 AF XY: 0.000802 AC XY: 54 AN XY: 67358

Gnomad4 AFR AF: 0.00137

Gnomad4 AMR AF: 0.000210

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00181

Gnomad4 SAS AF: 0.00436

Gnomad4 FIN AF: 0.000191

Gnomad4 NFE AF: 0.000351

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000675 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 01, 2025

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	-0.78
CADD	Benign	0.82
DANN	Benign	0.18

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: rs749508373; hg19: chr15-28632752;