Variant rs62357990 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_021942.6(TRAPPC11):c.897C>A(p.Ile299=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0611 in 1,611,224 control chromosomes in the GnomAD database, including 3,409 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. I299I) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.062 ( 359 hom., cov: 33)

Exomes 𝑓: 0.061 ( 3050 hom. )

Consequence

TRAPPC11
NM_021942.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.67

Variant links:

Genes affected

TRAPPC11 (HGNC:25751): (trafficking protein particle complex subunit 11) The protein encoded by this gene is a subunit of the TRAPP (transport protein particle) tethering complex, which functions in intracellular vesicle trafficking. This subunit is involved in early stage endoplasmic reticulum-to-Golgi vesicle transport. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2013]

TRAPPC11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 4-183679418-C-A is Benign according to our data. Variant chr4-183679418-C-A is described in ClinVar as [Benign]. Clinvar id is 261455.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-183679418-C-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.67 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC11	NM_021942.6 linkuse as main transcript	c.897C>A	p.Ile299=	synonymous_variant	9/30	ENST00000334690.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC11	ENST00000334690.11 linkuse as main transcript	c.897C>A	p.Ile299=	synonymous_variant	9/30	1	NM_021942.6	P1	Q7Z392-1
TRAPPC11	ENST00000357207.8 linkuse as main transcript	c.897C>A	p.Ile299=	synonymous_variant	9/31	1			Q7Z392-3
TRAPPC11	ENST00000505676.5 linkuse as main transcript	c.163-790C>A		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0617

AC:

9378

AN:

152096

Hom.:

358

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0511

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.0486

Gnomad ASJ

AF:

0.0703

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.0240

Gnomad FIN

AF:

0.0733

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0655

Gnomad OTH

AF:

0.0602

GnomAD3 exomes

AF:

0.0578

AC:

14437

AN:

249704

Hom.:

565

AF XY:

0.0564

AC XY:

7616

AN XY:

135030

show subpopulations

Gnomad AFR exome

AF:

0.0491

Gnomad AMR exome

AF:

0.0341

Gnomad ASJ exome

AF:

0.0671

Gnomad EAS exome

AF:

0.122

Gnomad SAS exome

AF:

0.0180

Gnomad FIN exome

AF:

0.0656

Gnomad NFE exome

AF:

0.0639

Gnomad OTH exome

AF:

0.0651

GnomAD4 exome

AF:

0.0610

AC:

89040

AN:

1459010

Hom.:

3050

Cov.:

AF XY:

0.0597

AC XY:

43334

AN XY:

725850

show subpopulations

Gnomad4 AFR exome

AF:

0.0462

Gnomad4 AMR exome

AF:

0.0365

Gnomad4 ASJ exome

AF:

0.0692

Gnomad4 EAS exome

AF:

0.0872

Gnomad4 SAS exome

AF:

0.0179

Gnomad4 FIN exome

AF:

0.0638

Gnomad4 NFE exome

AF:

0.0641

Gnomad4 OTH exome

AF:

0.0691

GnomAD4 genome

AF:

0.0616

AC:

9374

AN:

152214

Hom.:

359

Cov.:

AF XY:

0.0614

AC XY:

4571

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.0510

Gnomad4 AMR

AF:

0.0484

Gnomad4 ASJ

AF:

0.0703

Gnomad4 EAS

AF:

0.129

Gnomad4 SAS

AF:

0.0240

Gnomad4 FIN

AF:

0.0733

Gnomad4 NFE

AF:

0.0655

Gnomad4 OTH

AF:

0.0596

Alfa

AF:

0.0550

Hom.:

140

Bravo

AF:

0.0616

Asia WGS

AF:

0.0730

AC:

253

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 17, 2018

- -

Autosomal recessive limb-girdle muscular dystrophy type R18

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

2.0

DANN

Benign

0.79

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over