chrX-49606175-C-G

Variant names:

• chrX-49606175-C-G
• rs5906843
• NM_001040663.4:c.*160C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001040663.4(GAGE1):​c.*160C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., 0 hem., cov: 22)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: GAGE1 NM_001040663.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 3 publications found

Genes affected

GAGE1 (HGNC:4098): (G antigen 1) This gene belongs to a family of genes that are expressed in a variety of tumors but not in normal tissues, except for the testis. The sequences of the family members are highly related but differ by scattered nucleotide substitutions. The antigenic peptide YRPRPRRY, which is also encoded by several other family members, is recognized by autologous cytolytic T lymphocytes. Nothing is presently known about the function of this protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2010]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAGE1	NM_001040663.4	c.*160C>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000381700.11	NP_001035753.1
GAGE1	NR_102272.2	n.780C>G		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAGE1	ENST00000381700.11	c.*160C>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_001040663.4	ENSP00000371119.5
GAGE1	ENST00000381709.6	n.*237C>G		non_coding_transcript_exon_variant	Exon 6 of 6	2		ENSP00000371128.2
GAGE1	ENST00000381709.6	n.*237C>G		3_prime_UTR_variant	Exon 6 of 6	2		ENSP00000371128.2

Frequencies

GnomAD3 genomes AF: 0.00000912 AC: 1 AN: 109689 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.0000329

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

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 188845 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 48213

African (AFR) AF: 0.00 AC: 0 AN: 5379

American (AMR) AF: 0.00 AC: 0 AN: 7872

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4847

East Asian (EAS) AF: 0.00 AC: 0 AN: 15220

South Asian (SAS) AF: 0.00 AC: 0 AN: 4196

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23568

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 633

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 116737

Other (OTH) AF: 0.00 AC: 0 AN: 10393

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 109720 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 32146

African (AFR) AF: 0.00 AC: 0 AN: 30476

American (AMR) AF: 0.00 AC: 0 AN: 10244

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2631

East Asian (EAS) AF: 0.00 AC: 0 AN: 3475

South Asian (SAS) AF: 0.00 AC: 0 AN: 2590

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5496

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 211

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 52456

Other (OTH) AF: 0.00 AC: 0 AN: 1493

Alfa AF: 0.00 Hom.: 6710

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.34
DANN	Benign	0.32
PhyloP100		0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5906843; hg19: chrX-49370778;