Variant chr7-143756089-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_StrongBP6_Moderate

The NM_178561.5(CTAGE6):c.1570G>T(p.Ala524Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00039 ( 0 hom., cov: 9)

Exomes 𝑓: 0.00096 ( 45 hom. )

Failed GnomAD Quality Control

Consequence

CTAGE6
NM_178561.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.965

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PP2

Missense variant where missense usually causes diseases, CTAGE6

BP4

Computational evidence support a benign effect (MetaRNN=0.00538826).

BP6

Variant 7-143756089-C-A is Benign according to our data. Variant chr7-143756089-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2658120.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTAGE6	NM_178561.5 linkuse as main transcript	c.1570G>T	p.Ala524Ser	missense_variant	1/1	ENST00000470691.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTAGE6	ENST00000470691.2 linkuse as main transcript	c.1570G>T	p.Ala524Ser	missense_variant	1/1		NM_178561.5	P1
	ENST00000700950.1 linkuse as main transcript	n.178+13009G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

77308

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0000929

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000316

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00369

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000544

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000817

AC:

AN:

66094

Hom.:

AF XY:

0.000982

AC XY:

AN XY:

33612

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000643

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000125

Gnomad SAS exome

AF:

0.00400

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000709

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000964

AC:

1000

AN:

1037796

Hom.:

Cov.:

AF XY:

0.00120

AC XY:

617

AN XY:

514880

show subpopulations

Gnomad4 AFR exome

AF:

0.0000835

Gnomad4 AMR exome

AF:

0.000814

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.000706

Gnomad4 SAS exome

AF:

0.00546

Gnomad4 FIN exome

AF:

0.0000791

Gnomad4 NFE exome

AF:

0.000751

Gnomad4 OTH exome

AF:

0.000936

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000388

AC:

AN:

77380

Hom.:

Cov.:

AF XY:

0.000285

AC XY:

AN XY:

35100

show subpopulations

Gnomad4 AFR

AF:

0.0000925

Gnomad4 AMR

AF:

0.000315

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00370

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000544

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000391

Hom.:

ExAC

AF:

0.0000475

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2024

CTAGE6: PP2, BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.64

CADD

Benign

0.010

DANN

Benign

0.38

DEOGEN2

Benign

0.046

FATHMM_MKL

Benign

0.0025

M_CAP

Benign

0.041

MetaRNN

Benign

0.0054

MutationAssessor

Benign

-2.9

PrimateAI

Uncertain

0.48

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.043

MVP

0.15

GERP RS

-0.22

Varity_R

0.076

gMVP

0.30

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