X-49311781-A-T

Variant names:

• chrX-49311781-A-T
• rs11798415
• NM_001098413.4:c.203-5382A>T

Variant summary

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

The NM_001098413.4(GAGE10):​c.203-5382A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 110,913 control chromosomes in the GnomAD database, including 9,121 homozygotes. There are 14,337 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 (9121 hom., 14337 hem., cov: 23)
• Consequence: GAGE10 NM_001098413.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

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=-0.92).
• 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 rank	MANE	Protein	UniProt
GAGE10	NM_001098413.4	c.203-5382A>T		intron_variant	Intron 3 of 4	ENST00000407599.4	NP_001091883.3
GAGE10	XM_024452325.1	c.161-5382A>T		intron_variant	Intron 1 of 2		XP_024308093.1
LOC124905188	XR_007068231.1	n.639-1913A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAGE10	ENST00000407599.4	c.203-5382A>T		intron_variant	Intron 3 of 4	5	NM_001098413.4	ENSP00000385415.3

Frequencies

GnomAD3 genomes AF: 0.442 AC: 49021 AN: 110861 Hom.: 9120 Cov.: 23 AF XY: 0.432 AC XY: 14314 AN XY: 33119

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.576

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: 0.442 AC: 49036 AN: 110913 Hom.: 9121 Cov.: 23 AF XY: 0.432 AC XY: 14337 AN XY: 33181

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.479

Alfa AF: 0.499 Hom.: 3687

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
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: rs11798415; hg19: chrX-49168260;