X-49317261-C-G

Variant names:

• chrX-49317261-C-G
• rs782659658
• NM_001098413.4:c.301C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001098413.4(GAGE10):​c.301C>G​(p.Pro101Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. P101T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 22)
• Consequence: GAGE10 NM_001098413.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 0 publications found

Genes affected

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

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.061548084).

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.301C>G	p.Pro101Ala	missense	Exon 4 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.301C>G	p.Pro101Ala	missense	Exon 4 of 5	ENSP00000385415.3	A6NGK3

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.50	T
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.039
DANN	Benign	0.78
FATHMM_MKL	Benign	0.0068	N
M_CAP	Benign	0.0010	T
MetaRNN	Benign	0.062	T
MetaSVM	Benign	-1.0	T
PhyloP100		0.10
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-1.1	N
REVEL	Benign	0.020
Sift	Benign	0.92	T
Sift4G	Benign	0.18	T
Vest4		0.20
MutPred		0.25		Loss of stability (P = 0.084)
MVP		0.11
MPC		0.046
ClinPred		0.072	T
GERP RS		0.51
gMVP		0.0054
Mutation Taster		=98/2	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs782659658; hg19: chrX-49173740; COSMIC: COSV68163789; COSMIC: COSV68163789;