chrX-49552495-G-A

Position:

• chrX-49552495-G-A

Variant summary

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

The NM_001098418.3(GAGE12E):​c.52G>A​(p.Val18Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/15 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: GAGE12E NM_001098418.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

Genes affected

GAGE12E (HGNC:31905): (G antigen 12E)

GAGE12F (HGNC:31906): (G antigen 12F)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0968554).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAGE12E	NM_001098418.3	c.52G>A	p.Val18Ile	missense_variant	2/5	ENST00000381698.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAGE12E	ENST00000381698.5	c.52G>A	p.Val18Ile	missense_variant	2/5	1	NM_001098418.3	P1
GAGE12F	ENST00000639028.1	c.-9+1099G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.58	T
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.67
FATHMM_MKL	Benign	0.0051	N
M_CAP	Uncertain	0.23	D
MetaRNN	Benign	0.097	T
MetaSVM	Benign	-0.93	T
MutationTaster	Benign	1.0	N
PROVEAN	Benign	-0.23	N
REVEL	Benign	0.012
Sift	Benign	0.17	T
Sift4G	Benign	0.46	T
Vest4		0.057
MutPred		0.37		Loss of MoRF binding (P = 0.1197);
MVP		0.030
ClinPred		0.21	T
GERP RS		-0.00032

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-49317098;