chr9-124914953-T-C

Variant names:

• chr9-124914953-T-C
• rs646527
• NM_002077.4:c.844-2927A>G

Variant summary

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

The NM_002077.4(GOLGA1):​c.844-2927A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,106 control chromosomes in the GnomAD database, including 9,552 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 0.34 (9552 hom., cov: 32)
• Consequence: GOLGA1 NM_002077.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 3 publications found

Genes affected

GOLGA1 (HGNC:4424): (golgin A1) 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 encoded protein is associated with Sjogren's syndrome. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA1	NM_002077.4	c.844-2927A>G		intron_variant	Intron 10 of 22	ENST00000373555.9	NP_002068.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA1	ENST00000373555.9	c.844-2927A>G		intron_variant	Intron 10 of 22	1	NM_002077.4	ENSP00000362656.4
GOLGA1	ENST00000485337.1	n.172-2927A>G		intron_variant	Intron 2 of 9	5		ENSP00000435006.1
GOLGA1	ENST00000475407.5	n.494-2927A>G		intron_variant	Intron 5 of 17	5		ENSP00000473648.1

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51936 AN: 151988 Hom.: 9552 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.342 AC: 51945 AN: 152106 Hom.: 9552 Cov.: 32 AF XY: 0.332 AC XY: 24719 AN XY: 74362

African (AFR) AF: 0.232 AC: 9614 AN: 41490

American (AMR) AF: 0.325 AC: 4970 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1873 AN: 5176

South Asian (SAS) AF: 0.348 AC: 1680 AN: 4824

European-Finnish (FIN) AF: 0.241 AC: 2551 AN: 10586

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28679 AN: 67968

Other (OTH) AF: 0.350 AC: 739 AN: 2114

Alfa AF: 0.371 Hom.: 1783

Bravo AF: 0.344

Asia WGS AF: 0.348 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.41
PhyloP100		0.056
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: rs646527; hg19: chr9-127677232;