rs28555639

chr19-45173106-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001270891.2(TRAPPC6A):c.84+5029A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 151,354 control chromosomes in the GnomAD database, including 1,610 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 0.13 (1610 hom., cov: 31)
• Consequence: TRAPPC6A NM_001270891.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

Genes affected

TRAPPC6A (HGNC:23069): (trafficking protein particle complex subunit 6A) This gene encodes a component of the trafficking protein particle complex, which tethers transport vesicles to the cis-Golgi membrane. Loss of expression of the related gene in mouse affects coat and eye pigmentation, suggesting that the encoded protein may be involved in melanosome biogenesis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2012]

MARK4 (HGNC:13538): (microtubule affinity regulating kinase 4) This gene encodes a member of the microtubule affinity-regulating kinase family. These protein kinases phosphorylate microtubule-associated proteins and regulate the transition between stable and dynamic microtubules. The encoded protein is associated with the centrosome throughout mitosis and may be involved in cell cycle control. Expression of this gene is a potential marker for cancer, and the encoded protein may also play a role in Alzheimer's disease. Pseudogenes of this gene are located on both the short and long arm of chromosome 3. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC6A	NM_001270891.2	c.84+5029A>T		intron_variant		ENST00000585934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC6A	ENST00000585934.1	c.84+5029A>T		intron_variant		1	NM_001270891.2	P1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20371 AN: 151236 Hom.: 1609 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0953

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.135 AC: 20377 AN: 151354 Hom.: 1610 Cov.: 31 AF XY: 0.132 AC XY: 9777 AN XY: 73994

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0953

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.148

Alfa AF: 0.134 Hom.: 214

Bravo AF: 0.136

Asia WGS AF: 0.159 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.43
Dann	Benign	0.53

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: rs28555639; hg19: chr19-45676364;