X-49336346-C-T

Variant names:

• chrX-49336346-C-T
• NM_001098412.4:c.305C>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001098412.4(GAGE13):​c.305C>T​(p.Pro102Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 9/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: GAGE13 NM_001098412.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.880

Genes affected

GAGE13 (HGNC:29081): (G antigen 13)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.1333664).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAGE13	NM_001098412.4	c.305C>T	p.Pro102Leu	missense_variant	Exon 4 of 5	ENST00000612958.2	NP_001091882.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAGE13	ENST00000612958.2	c.305C>T	p.Pro102Leu	missense_variant	Exon 4 of 5	1	NM_001098412.4	ENSP00000483811.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Apr 09, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.305C>T (p.P102L) alteration is located in exon 4 (coding exon 3) of the GAGE13 gene. This alteration results from a C to T substitution at nucleotide position 305, causing the proline (P) at amino acid position 102 to be replaced by a leucine (L). 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	0.11
BayesDel_addAF	Benign	-0.42	T
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.96
DEOGEN2	Benign	0.024	T
FATHMM_MKL	Benign	0.00049	N
LIST_S2	Benign	0.68	T
M_CAP	Uncertain	0.094	D
MetaRNN	Benign	0.13	T
MetaSVM	Benign	-1.1	T
Sift4G	Uncertain	0.0070	D
Vest4		0.044
MVP		0.18
ClinPred		0.68	D
GERP RS		-2.5
Varity_R		0.059
gMVP		0.0045

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-49202318;