7-143572579-C-G

Variant names:

• chr7-143572579-C-G
• rs1279500595
• NM_001008747.2:c.762C>G

Variant summary

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

The NM_001008747.2(CTAGE15):​c.762C>G​(p.His254Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000016 (0 hom., cov: 16)
  • Failed GnomAD Quality Control
• Consequence: CTAGE15 NM_001008747.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.0330

Genes affected

CTAGE15 (HGNC:37295): (CTAGE family member 15) 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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.06704712).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTAGE15	NM_001008747.2	c.762C>G	p.His254Gln	missense_variant	Exon 1 of 1	ENST00000420911.2	NP_001008747.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTAGE15	ENST00000420911.2	c.762C>G	p.His254Gln	missense_variant	Exon 1 of 1	6	NM_001008747.2	ENSP00000474204.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2 AN: 124902 Hom.: 0 Cov.: 16 FAILED QC

Gnomad AFR AF: 0.0000599

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 19

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000160 AC: 2 AN: 124902 Hom.: 0 Cov.: 16 AF XY: 0.0000333 AC XY: 2 AN XY: 60106

Gnomad4 AFR AF: 0.0000599

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 23, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.762C>G (p.H254Q) alteration is located in exon 1 (coding exon 1) of the CTAGE15 gene. This alteration results from a C to G substitution at nucleotide position 762, causing the histidine (H) at amino acid position 254 to be replaced by a glutamine (Q). 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	0.14
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	3.5
DANN	Benign	0.50
DEOGEN2	Benign	0.0036	T
FATHMM_MKL	Benign	0.0055	N
M_CAP	Benign	0.0084	T
MetaRNN	Benign	0.067	T
MutationAssessor	Benign	1.4	L
PrimateAI	Uncertain	0.58	T
Sift4G	Benign	0.33	T
Polyphen		0.0090	B
Vest4		0.14
MVP		0.043
Varity_R		0.16
gMVP		0.054

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

Other links and lift over

dbSNP: rs1279500595; hg19: chr7-143269672;