rs12498138

Variant names:

• chr3-121740742-G-A
• rs12498138
• NM_001366282.2:c.-3+8890C>T

Variant summary

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

The NM_001366282.2(GOLGB1):​c.-3+8890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0845 in 152,186 control chromosomes in the GnomAD database, including 1,191 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 0.085 (1191 hom., cov: 32)
• Consequence: GOLGB1 NM_001366282.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 15 publications found

Genes affected

GOLGB1 (HGNC:4429): (golgin B1) Enables RNA binding activity. Involved in protein localization to pericentriolar material. Located in Golgi apparatus and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGB1	NM_001366282.2	c.-3+8890C>T		intron_variant	Intron 1 of 21	ENST00000614479.5	NP_001353211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGB1	ENST00000614479.5	c.-3+8890C>T		intron_variant	Intron 1 of 21	1	NM_001366282.2	ENSP00000484083.2

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 12833 AN: 152068 Hom.: 1176 Cov.: 32

Gnomad AFR AF: 0.0196

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.0466

Gnomad FIN AF: 0.0903

Gnomad MID AF: 0.0353

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.0800

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

GnomAD4 genome AF: 0.0845 AC: 12861 AN: 152186 Hom.: 1191 Cov.: 32 AF XY: 0.0896 AC XY: 6665 AN XY: 74398

African (AFR) AF: 0.0196 AC: 814 AN: 41572

American (AMR) AF: 0.292 AC: 4451 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3470

East Asian (EAS) AF: 0.0813 AC: 422 AN: 5188

South Asian (SAS) AF: 0.0466 AC: 225 AN: 4828

European-Finnish (FIN) AF: 0.0903 AC: 954 AN: 10562

Middle Eastern (MID) AF: 0.0379 AC: 11 AN: 290

European-Non Finnish (NFE) AF: 0.0826 AC: 5617 AN: 67990

Other (OTH) AF: 0.0801 AC: 169 AN: 2110

Alfa AF: 0.0874 Hom.: 2735

Bravo AF: 0.0989

Asia WGS AF: 0.0750 AC: 258 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.52
PhyloP100		0.36
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: rs12498138; hg19: chr3-121459589;