3-37248331-C-T

Variant names:

• chr3-37248331-C-T
• rs336597
• NM_002078.5:c.73-3064C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002078.5(GOLGA4):​c.73-3064C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,210 control chromosomes in the GnomAD database, including 56,219 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.85 (56219 hom., cov: 31)
• Consequence: GOLGA4 NM_002078.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 5 publications found

Genes affected

GOLGA4 (HGNC:4427): (golgin A4) The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked cisternae (flattened membrane sacs). Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. This gene encodes one of the golgins, a family of proteins localized to the Golgi. This protein has been postulated to play a role in Rab6-regulated membrane-tethering events in the Golgi apparatus. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, Feb 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA4	NM_002078.5	c.73-3064C>T		intron_variant	Intron 1 of 23	ENST00000361924.7	NP_002069.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA4	ENST00000361924.7	c.73-3064C>T		intron_variant	Intron 1 of 23	1	NM_002078.5	ENSP00000354486.2

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129919 AN: 152092 Hom.: 56174 Cov.: 31

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.871

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.854 AC: 130025 AN: 152210 Hom.: 56219 Cov.: 31 AF XY: 0.847 AC XY: 63011 AN XY: 74426

African (AFR) AF: 0.969 AC: 40260 AN: 41546

American (AMR) AF: 0.845 AC: 12924 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3142 AN: 3472

East Asian (EAS) AF: 0.653 AC: 3378 AN: 5170

South Asian (SAS) AF: 0.680 AC: 3280 AN: 4820

European-Finnish (FIN) AF: 0.715 AC: 7571 AN: 10582

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56609 AN: 68008

Other (OTH) AF: 0.869 AC: 1835 AN: 2112

Alfa AF: 0.847 Hom.: 171061

Bravo AF: 0.871

Asia WGS AF: 0.707 AC: 2459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.065
DANN	Benign	0.23
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs336597; hg19: chr3-37289822;