rs201726759

Variant names:

• chr5-65637736-G-A
• rs201726759
• NM_024941.4:c.256G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-65637736-G-A
• chr5-65637736-G-C
• chr5-65637736-G-T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_024941.4(TRAPPC13):​c.256G>A​(p.Val86Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,572,286 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00011 (0 hom., cov: 30)
  • Exomes 𝑓: 0.00015 (1 hom.)
• Consequence: TRAPPC13 NM_024941.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 9.24
• Publications: 6 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: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.34630376).

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.256G>A	p.Val86Ile	missense	Exon 4 of 13	NP_079217.2	A5PLN9-1
	TRAPPC13	NM_001093755.2		c.256G>A	p.Val86Ile	missense	Exon 4 of 13	NP_001087224.1	A5PLN9-5
	TRAPPC13	NM_001243737.2		c.256G>A	p.Val86Ile	missense	Exon 4 of 12	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.256G>A	p.Val86Ile	missense	Exon 4 of 13	ENSP00000382367.3	A5PLN9-1
	TRAPPC13	ENST00000438419.6	TSL:1	c.256G>A	p.Val86Ile	missense	Exon 4 of 13	ENSP00000409231.2	A5PLN9-5
	TRAPPC13	ENST00000505553.5	TSL:1	c.256G>A	p.Val86Ile	missense	Exon 4 of 12	ENSP00000423405.1	A5PLN9-4

Frequencies

GnomAD3 genomes AF: 0.000112 AC: 17 AN: 151822 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.0000484

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000656

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000177

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000912 AC: 21 AN: 230220 AF XY: 0.0000879

Gnomad AFR exome AF: 0.0000679

Gnomad AMR exome AF: 0.0000339

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000149

Gnomad OTH exome AF: 0.000179

GnomAD4 exome AF: 0.000152 AC: 216 AN: 1420464 Hom.: 1 Cov.: 26 AF XY: 0.000163 AC XY: 115 AN XY: 707566

African (AFR) AF: 0.0000319 AC: 1 AN: 31360

American (AMR) AF: 0.0000255 AC: 1 AN: 39202

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25338

East Asian (EAS) AF: 0.000103 AC: 4 AN: 38904

South Asian (SAS) AF: 0.0000860 AC: 7 AN: 81390

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52872

Middle Eastern (MID) AF: 0.000178 AC: 1 AN: 5632

European-Non Finnish (NFE) AF: 0.000178 AC: 194 AN: 1087004

Other (OTH) AF: 0.000136 AC: 8 AN: 58762

GnomAD4 genome AF: 0.000112 AC: 17 AN: 151822 Hom.: 0 Cov.: 30 AF XY: 0.000135 AC XY: 10 AN XY: 74140

African (AFR) AF: 0.0000484 AC: 2 AN: 41318

American (AMR) AF: 0.0000656 AC: 1 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4804

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10524

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.000177 AC: 12 AN: 67976

Other (OTH) AF: 0.00 AC: 0 AN: 2088

Alfa AF: 0.000223 Hom.: 0

Bravo AF: 0.000125

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000246 AC: 2

ExAC AF: 0.0000828 AC: 10

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.099	T
BayesDel_noAF	Uncertain	-0.060
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.022	T
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.93	D
M_CAP	Benign	0.0072	T
MetaRNN	Benign	0.35	T
MetaSVM	Benign	-0.60	T
MutationAssessor	Benign	0.98	L
PhyloP100		9.2
PrimateAI	Pathogenic	0.81	D
PROVEAN	Benign	-0.53	N
REVEL	Benign	0.29
Sift	Benign	0.047	D
Sift4G	Benign	0.16	T
Polyphen		0.11	B
Vest4		0.64
MVP		0.15
MPC		0.36
ClinPred		0.076	T
GERP RS		5.8
Varity_R		0.097
gMVP		0.20
Mutation Taster		=79/21	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs201726759; hg19: chr5-64933563;