rs1919555

Positions:

• chr3-121728053-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
GOLGB1	NM_001366282.2	c.403-1012C>T		intron_variant		ENST00000614479.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGB1	ENST00000614479.5	c.403-1012C>T		intron_variant		1	NM_001366282.2	P3

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

Gnomad4 AFR AF: 0.0102

Gnomad4 AMR AF: 0.0481

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0189

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0578

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0561 Hom.: 370

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

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: rs1919555; hg19: chr3-121446900;