rs5906782

Positions:

• chrX-49316820-C-G
• chrX-49316820-C-T

Variant summary

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

The NM_001098413.4(GAGE10):​c.203-343C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 109,797 control chromosomes in the GnomAD database, including 9,093 homozygotes. There are 13,990 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 (9093 hom., 13990 hem., cov: 22)
• Consequence: GAGE10 NM_001098413.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAGE10	NM_001098413.4	c.203-343C>G		intron_variant		ENST00000407599.4	NP_001091883.3
GAGE10	XM_024452325.1	c.161-343C>G		intron_variant			XP_024308093.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAGE10	ENST00000407599.4	c.203-343C>G		intron_variant		5	NM_001098413.4	ENSP00000385415	P1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 48604 AN: 109745 Hom.: 9092 Cov.: 22 AF XY: 0.435 AC XY: 13964 AN XY: 32115

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.572

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.443 AC: 48622 AN: 109797 Hom.: 9093 Cov.: 22 AF XY: 0.435 AC XY: 13990 AN XY: 32177

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.480

Alfa AF: 0.310 Hom.: 1478

Bravo AF: 0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.21
DANN	Benign	0.52

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: rs5906782; hg19: chrX-49173299;