chr3-121728053-G-A

Variant names:

• chr3-121728053-G-A
• rs1919555
• NM_001366282.2:c.403-1012C>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.403-1012C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 152,258 control chromosomes in the GnomAD database, including 203 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 0.044 (203 hom., cov: 31)
• Consequence: GOLGB1 NM_001366282.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 7 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGB1	NM_001366282.2	c.403-1012C>T		intron_variant	Intron 4 of 21	ENST00000614479.5	NP_001353211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGB1	ENST00000614479.5	c.403-1012C>T		intron_variant	Intron 4 of 21	1	NM_001366282.2	ENSP00000484083.2

Frequencies

GnomAD3 genomes AF: 0.0444 AC: 6755 AN: 152140 Hom.: 203 Cov.: 31

Gnomad AFR AF: 0.0102

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0578

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0444 AC: 6753 AN: 152258 Hom.: 203 Cov.: 31 AF XY: 0.0454 AC XY: 3381 AN XY: 74448

African (AFR) AF: 0.0102 AC: 424 AN: 41542

American (AMR) AF: 0.0481 AC: 735 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0189 AC: 91 AN: 4826

European-Finnish (FIN) AF: 0.100 AC: 1062 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0578 AC: 3928 AN: 68016

Other (OTH) AF: 0.0497 AC: 105 AN: 2114

Alfa AF: 0.0544 Hom.: 472

Bravo AF: 0.0409

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.94
DANN	Benign	0.18
PhyloP100		0.021
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: rs1919555; hg19: chr3-121446900;