2-85319492-C-T

Variant names:

• chr2-85319492-C-T
• rs1061782
• NM_006464.4:c.*3244G>A

Variant summary

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

The ENST00000377386.8(TGOLN2):​c.*3244G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,874 control chromosomes in the GnomAD database, including 26,725 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 0.59 (26723 hom., cov: 31)
  • Exomes 𝑓: 0.75 (2 hom.)
• Consequence: TGOLN2 ENST00000377386.8 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 21 publications found

Genes affected

TGOLN2 (HGNC:15450): (trans-golgi network protein 2) This gene encodes a type I integral membrane protein that is localized to the trans-Golgi network, a major sorting station for secretory and membrane proteins. The encoded protein cycles between early endosomes and the trans-Golgi network, and may play a role in exocytic vesicle formation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377386.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TGOLN2	NM_006464.4	MANE Select	c.*3244G>A		3_prime_UTR	Exon 4 of 4	NP_006455.2
	TGOLN2	NM_001368095.1		c.*3251G>A		3_prime_UTR	Exon 4 of 4	NP_001355024.1
	TGOLN2	NM_001368096.1		c.*3213G>A		3_prime_UTR	Exon 4 of 4	NP_001355025.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TGOLN2	ENST00000377386.8	TSL:1 MANE Select	c.*3244G>A		3_prime_UTR	Exon 4 of 4	ENSP00000366603.3
	TGOLN2	ENST00000398263.6	TSL:1	c.*3244G>A		3_prime_UTR	Exon 5 of 5	ENSP00000381312.2

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88854 AN: 151748 Hom.: 26700 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.617

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 2 Cov.: 0 AF XY: 0.750 AC XY: 6 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.833 AC: 5 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.586 AC: 88923 AN: 151866 Hom.: 26723 Cov.: 31 AF XY: 0.593 AC XY: 44046 AN XY: 74228

African (AFR) AF: 0.572 AC: 23689 AN: 41408

American (AMR) AF: 0.691 AC: 10534 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2308 AN: 3468

East Asian (EAS) AF: 0.960 AC: 4953 AN: 5162

South Asian (SAS) AF: 0.646 AC: 3104 AN: 4804

European-Finnish (FIN) AF: 0.594 AC: 6259 AN: 10532

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36061 AN: 67934

Other (OTH) AF: 0.620 AC: 1311 AN: 2114

Alfa AF: 0.562 Hom.: 34857

Bravo AF: 0.598

Asia WGS AF: 0.792 AC: 2751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.3
DANN	Benign	0.85
PhyloP100		-0.21
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: rs1061782; hg19: chr2-85546615;