X-49311069-A-G

Variant names:

• chrX-49311069-A-G
• rs5906777
• NM_001098413.4:c.202+5545A>G

Variant summary

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

The NM_001098413.4(GAGE10):​c.202+5545A>G 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 109,100 control chromosomes in the GnomAD database, including 9,066 homozygotes. There are 13,448 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 (9066 hom., 13448 hem., cov: 22)
• Consequence: GAGE10 NM_001098413.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

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=-0.93).
• 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 rank	MANE	Protein	UniProt
GAGE10	NM_001098413.4	c.202+5545A>G		intron_variant	Intron 3 of 4	ENST00000407599.4	NP_001091883.3
GAGE10	XM_024452325.1	c.160+5545A>G		intron_variant	Intron 1 of 2		XP_024308093.1
LOC124905188	XR_007068231.1	n.638+2587A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAGE10	ENST00000407599.4	c.202+5545A>G		intron_variant	Intron 3 of 4	5	NM_001098413.4	ENSP00000385415.3

Frequencies

GnomAD3 genomes AF: 0.440 AC: 47984 AN: 109043 Hom.: 9065 Cov.: 22 AF XY: 0.426 AC XY: 13419 AN XY: 31473

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.584

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.440 AC: 48005 AN: 109100 Hom.: 9066 Cov.: 22 AF XY: 0.426 AC XY: 13448 AN XY: 31540

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.474

Alfa AF: 0.227 Hom.: 903

Bravo AF: 0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.79

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: rs5906777; hg19: chrX-49167548;