X-49308401-T-C

Position:

• chrX-49308401-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001098413.4(GAGE10):​c.202+2877T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 110,865 control chromosomes in the GnomAD database, including 9,054 homozygotes. There are 14,280 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (9054 hom., 14280 hem., cov: 23)
• Consequence: GAGE10 NM_001098413.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

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

LOC124905188 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAGE10	NM_001098413.4	c.202+2877T>C		intron_variant		ENST00000407599.4	NP_001091883.3
GAGE10	XM_024452325.1	c.160+2877T>C		intron_variant			XP_024308093.1
LOC124905188	XR_007068231.1	n.557T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAGE10	ENST00000407599.4	c.202+2877T>C		intron_variant		5	NM_001098413.4	ENSP00000385415.3

Frequencies

GnomAD3 genomes AF: 0.440 AC: 48801 AN: 110811 Hom.: 9053 Cov.: 23 AF XY: 0.431 AC XY: 14254 AN XY: 33081

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.474

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.440 AC: 48818 AN: 110865 Hom.: 9054 Cov.: 23 AF XY: 0.431 AC XY: 14280 AN XY: 33145

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.479

Alfa AF: 0.497 Hom.: 3694

Bravo AF: 0.421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.54

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: rs4824755; hg19: chrX-49164880;