X-49319736-C-G

Variant names:

• chrX-49319736-C-G
• rs2066409583
• NM_001098413.4:c.337C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001098413.4(GAGE10):​c.337C>G​(p.Gln113Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q113K) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 16)
• Consequence: GAGE10 NM_001098413.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 0 publications found

Genes affected

GAGE10 (HGNC:30968): (G antigen 10)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.099035144).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098413.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAGE10	NM_001098413.4	MANE Select	c.337C>G	p.Gln113Glu	missense	Exon 5 of 5	NP_001091883.3	A6NGK3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAGE10	ENST00000407599.4	TSL:5 MANE Select	c.337C>G	p.Gln113Glu	missense	Exon 5 of 5	ENSP00000385415.3	A6NGK3

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Cov.: 16

GnomAD4 genome Cov.: 16

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.074
BayesDel_addAF	Benign	-0.56	T
BayesDel_noAF	Benign	-1.1
CADD	Benign	5.6
DANN	Benign	0.82
FATHMM_MKL	Benign	0.013	N
M_CAP	Benign	0.0013	T
MetaRNN	Benign	0.099	T
MetaSVM	Benign	-0.98	T
PhyloP100		-0.40
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-1.1	N
REVEL	Benign	0.024
Sift	Benign	0.22	T
Sift4G	Benign	0.25	T
Vest4		0.082
MutPred		0.38		Loss of helix (P = 0.0558)
MVP		0.21
MPC		0.011
ClinPred		0.13	T
GERP RS		-0.59
gMVP		0.0021
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2066409583; hg19: chrX-49176215;