chr14-39150383-T-TAA

Variant names:

• chr14-39150383-T-TAA
• rs150886646
• NM_001079537.2:c.446-4_446-3dupTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001079537.2(TRAPPC6B):​c.446-4_446-3dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000765 in 1,136,594 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.000077 (0 hom.)
• Consequence: TRAPPC6B NM_001079537.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

TRAPPC6B (HGNC:23066): (trafficking protein particle complex subunit 6B) TRAPPC6B is a component of TRAPP complexes, which are tethering complexes involved in vesicle transport (Kummel et al., 2005 [PubMed 16025134]).[supplied by OMIM, Mar 2008]

ENSG00000285830 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAPPC6B	NM_001079537.2	c.446-4_446-3dupTT		splice_region_variant, intron_variant	Intron 5 of 5	ENST00000330149.10	NP_001073005.1
TRAPPC6B	NM_177452.4	c.362-4_362-3dupTT		splice_region_variant, intron_variant	Intron 4 of 4		NP_803235.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAPPC6B	ENST00000330149.10	c.446-4_446-3dupTT		splice_region_variant, intron_variant	Intron 5 of 5	1	NM_001079537.2	ENSP00000330289.5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.0000765 AC: 87 AN: 1136594 Hom.: 0 Cov.: 19 AF XY: 0.0000780 AC XY: 44 AN XY: 563914

Gnomad4 AFR exome AF: 0.0000804

Gnomad4 AMR exome AF: 0.000157

Gnomad4 ASJ exome AF: 0.0000533

Gnomad4 EAS exome AF: 0.000205

Gnomad4 SAS exome AF: 0.0000484

Gnomad4 FIN exome AF: 0.0000314

Gnomad4 NFE exome AF: 0.0000710

Gnomad4 OTH exome AF: 0.000108

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs150886646; hg19: chr14-39619587;