Genetic Variant CTAGE6:p.Leu537Pro (chr7-143756049-A-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_178561.5(CTAGE6):c.1610T>C(p.Leu537Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00034 ( 0 hom., cov: 5)

Exomes 𝑓: 0.00053 ( 3 hom. )

Failed GnomAD Quality Control

Consequence

CTAGE6
NM_178561.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.78

Variant links:

Genes affected

CTAGE6 (HGNC:28644): (CTAGE family member 6) Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; protein secretion; and vesicle cargo loading. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum exit site and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

CTAGE6 links:

ENSG00000291149 (HGNC:):

ENSG00000291149 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007961482).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTAGE6	NM_178561.5 link	c.1610T>C	p.Leu537Pro	missense_variant	Exon 1 of 1	ENST00000470691.2	NP_848656.2	Q86UF2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTAGE6	ENST00000470691.2 link	c.1610T>C	p.Leu537Pro	missense_variant	Exon 1 of 1	6	NM_178561.5	ENSP00000474388.1		Q86UF2
ENSG00000291149	ENST00000700950.1 link	n.178+13049T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

43480

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000328

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000599

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000940

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000439

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000532

AC:

453

AN:

851972

Hom.:

Cov.:

AF XY:

0.000516

AC XY:

220

AN XY:

426206

show subpopulations

Gnomad4 AFR exome

AF:

0.000341

Gnomad4 AMR exome

AF:

0.00212

Gnomad4 ASJ exome

AF:

0.000127

Gnomad4 EAS exome

AF:

0.000428

Gnomad4 SAS exome

AF:

0.000417

Gnomad4 FIN exome

AF:

0.0000954

Gnomad4 NFE exome

AF:

0.000546

Gnomad4 OTH exome

AF:

0.000414

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000345

AC:

AN:

43480

Hom.:

Cov.:

AF XY:

0.000313

AC XY:

AN XY:

19156

show subpopulations

Gnomad4 AFR

AF:

0.000245

Gnomad4 AMR

AF:

0.000598

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000945

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000439

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000560

Hom.:

ExAC

AF:

0.0000578

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Apr 25, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1610T>C (p.L537P) alteration is located in exon 1 (coding exon 1) of the CTAGE6 gene. This alteration results from a T to C substitution at nucleotide position 1610, causing the leucine (L) at amino acid position 537 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.078

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

0.46

DEOGEN2

Benign

0.051

FATHMM_MKL

Benign

0.060

MetaRNN

Benign

0.0080

MutationAssessor

Uncertain

2.8

PrimateAI

Uncertain

0.58

Sift4G

Benign

0.28

Polyphen

0.35

Vest4

0.17

MVP

0.12

GERP RS

0.11

Varity_R

0.16

gMVP

0.64

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