chr5-65661859-A-G

Position:

• chr5-65661859-A-G

Variant summary

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

The NM_024941.4(TRAPPC13):​c.898-191A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 484,818 control chromosomes in the GnomAD database, including 94,840 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 0.61 (28983 hom., cov: 33)
  • Exomes 𝑓: 0.63 (65857 hom.)
• Consequence: TRAPPC13 NM_024941.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408

Genes affected

TRAPPC13 (HGNC:25828): (trafficking protein particle complex subunit 13) Predicted to be located in cytosol. Predicted to be part of TRAPPIII protein complex. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRAPPC13	NM_024941.4	c.898-191A>G		intron_variant		ENST00000399438.8	NP_079217.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAPPC13	ENST00000399438.8	c.898-191A>G		intron_variant		2	NM_024941.4	ENSP00000382367	A1

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93303 AN: 151908 Hom.: 28962 Cov.: 33

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.586

GnomAD4 exome AF: 0.625 AC: 208083 AN: 332792 Hom.: 65857 Cov.: 4 AF XY: 0.627 AC XY: 108909 AN XY: 173816

Gnomad4 AFR exome AF: 0.599

Gnomad4 AMR exome AF: 0.544

Gnomad4 ASJ exome AF: 0.580

Gnomad4 EAS exome AF: 0.418

Gnomad4 SAS exome AF: 0.670

Gnomad4 FIN exome AF: 0.652

Gnomad4 NFE exome AF: 0.647

Gnomad4 OTH exome AF: 0.624

GnomAD4 genome AF: 0.614 AC: 93362 AN: 152026 Hom.: 28983 Cov.: 33 AF XY: 0.610 AC XY: 45309 AN XY: 74308

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.582

Alfa AF: 0.621 Hom.: 4225

Bravo AF: 0.604

Asia WGS AF: 0.560 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.42

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: rs37347; hg19: chr5-64957686;