X-49316820-C-T

Variant names:

• chrX-49316820-C-T
• rs5906782
• NM_001098413.4:c.203-343C>T

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.203-343C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000911 in 109,813 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples 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 0.0000091 (0 hom., 0 hem., cov: 22)
• Consequence: GAGE10 NM_001098413.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 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 (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAGE10	NM_001098413.4	c.203-343C>T		intron_variant	Intron 3 of 4	ENST00000407599.4	NP_001091883.3
GAGE10	XM_024452325.1	c.161-343C>T		intron_variant	Intron 1 of 2		XP_024308093.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAGE10	ENST00000407599.4	c.203-343C>T		intron_variant	Intron 3 of 4	5	NM_001098413.4	ENSP00000385415.3

Frequencies

GnomAD3 genomes AF: 0.00000911 AC: 1 AN: 109813 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.0000330

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000911 AC: 1 AN: 109813 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 32147

African (AFR) AF: 0.0000330 AC: 1 AN: 30265

American (AMR) AF: 0.00 AC: 0 AN: 10219

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2619

East Asian (EAS) AF: 0.00 AC: 0 AN: 3460

South Asian (SAS) AF: 0.00 AC: 0 AN: 2525

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5664

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 229

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 52683

Other (OTH) AF: 0.00 AC: 0 AN: 1474

Alfa AF: 0.00 Hom.: 1478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.44
PhyloP100		-1.1

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

Other links and lift over

dbSNP: rs5906782; hg19: chrX-49173299;