2-3479432-TTC-CTT

Variant names:

• chr2-3479432-TTC-CTT
• NM_016030.6:c.2179_2181delTTCinsCTT
• TRAPPC12 p.Phe727Leu

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_016030.6(TRAPPC12):​c.2179_2181delTTCinsCTT​(p.Phe727Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. The variant is present in control chromosomes in GnomAd MNV project. The variant allele was found at a frequency of 0.00000399 in 1 alleles, including 0 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. F727F) has been classified as Benign.

• Frequency: GnomAD MNV: 𝑓 0.0000040 Genomes: not found (cov: 34)
• Consequence: TRAPPC12 NM_016030.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.67
• Publications: 0 publications found

Genes affected

TRAPPC12 (HGNC:24284): (trafficking protein particle complex subunit 12) Involved in several processes, including endoplasmic reticulum to Golgi vesicle-mediated transport; positive regulation of protein localization to kinetochore; and regulation of kinetochore assembly. Located in Golgi apparatus; kinetochore; and nucleoplasm. Part of TRAPP complex. Colocalizes with endoplasmic reticulum-Golgi intermediate compartment and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TRAPPC12-AS1 (HGNC:41046): (TRAPPC12 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016030.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAPPC12	NM_016030.6	MANE Select	c.2179_2181delTTCinsCTT	p.Phe727Leu	missense	N/A	NP_057114.5
	TRAPPC12	NM_001321102.2		c.2179_2181delTTCinsCTT	p.Phe727Leu	missense	N/A	NP_001308031.1	Q8WVT3
	TRAPPC12-AS1	NR_046720.1		n.3560_3562delGAAinsAAG		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAPPC12	ENST00000324266.10	TSL:1 MANE Select	c.2179_2181delTTCinsCTT	p.Phe727Leu	missense	N/A	ENSP00000324318.5	Q8WVT3
	TRAPPC12	ENST00000858088.1		c.2353_2355delTTCinsCTT	p.Phe785Leu	missense	N/A	ENSP00000528147.1
	TRAPPC12	ENST00000964175.1		c.2284_2286delTTCinsCTT	p.Phe762Leu	missense	N/A	ENSP00000634234.1

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

GnomAD MNV AF: 0.00000399 AC: 1 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr2-3483203;