5-65661859-A-G

Variant names:

• chr5-65661859-A-G
• rs37347
• NM_024941.4:c.898-191A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024941.4. 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
	TRAPPC13	NM_024941.4	MANE Select	c.898-191A>G		intron	N/A	NP_079217.2	A5PLN9-1
	TRAPPC13	NM_001093755.2		c.898-191A>G		intron	N/A	NP_001087224.1	A5PLN9-5
	TRAPPC13	NM_001243737.2		c.880-191A>G		intron	N/A	NP_001230666.1	A5PLN9-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAPPC13	ENST00000399438.8	TSL:2 MANE Select	c.898-191A>G		intron	N/A	ENSP00000382367.3	A5PLN9-1
	TRAPPC13	ENST00000438419.6	TSL:1	c.898-191A>G		intron	N/A	ENSP00000409231.2	A5PLN9-5
	TRAPPC13	ENST00000505553.5	TSL:1	c.880-191A>G		intron	N/A	ENSP00000423405.1	A5PLN9-4

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

African (AFR) AF: 0.599 AC: 4695 AN: 7840

American (AMR) AF: 0.544 AC: 5004 AN: 9202

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 6299 AN: 10866

East Asian (EAS) AF: 0.418 AC: 9669 AN: 23108

South Asian (SAS) AF: 0.670 AC: 16329 AN: 24362

European-Finnish (FIN) AF: 0.652 AC: 17163 AN: 26314

Middle Eastern (MID) AF: 0.592 AC: 1612 AN: 2724

European-Non Finnish (NFE) AF: 0.647 AC: 134579 AN: 207978

Other (OTH) AF: 0.624 AC: 12733 AN: 20398

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

African (AFR) AF: 0.612 AC: 25359 AN: 41470

American (AMR) AF: 0.538 AC: 8199 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2002 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2251 AN: 5178

South Asian (SAS) AF: 0.646 AC: 3117 AN: 4828

European-Finnish (FIN) AF: 0.639 AC: 6744 AN: 10546

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43683 AN: 67966

Other (OTH) AF: 0.582 AC: 1229 AN: 2110

Alfa AF: 0.621 Hom.: 4374

Bravo AF: 0.604

Asia WGS AF: 0.560 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.42
PhyloP100		0.41
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: rs37347; hg19: chr5-64957686;