Genetic Variant GAGE1:c.*160C>A (chrX-49606175-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001040663.4(GAGE1):c.*160C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 297,463 control chromosomes in the GnomAD database, including 30,815 homozygotes. There are 42,522 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 ( 9041 hom., 13615 hem., cov: 22)

Exomes 𝑓: 0.56 ( 21774 hom. 28907 hem. )

Consequence

GAGE1
NM_001040663.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.340

Publications

3 publications found

Variant links:

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]

GAGE1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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
GAGE1	NM_001040663.4 link	c.*160C>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000381700.11	NP_001035753.1	P0DTW1A0A158RFV5
GAGE1	NR_102272.2 link	n.780C>A		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GAGE1	ENST00000381700.11 link	c.*160C>A	3_prime_UTR_variant	Exon 5 of 5	1	NM_001040663.4	ENSP00000371119.5	P0DTW1
GAGE1	ENST00000381709.6 link	n.*237C>A	non_coding_transcript_exon_variant	Exon 6 of 6	2		ENSP00000371128.2
GAGE1	ENST00000381709.6 link	n.*237C>A	3_prime_UTR_variant	Exon 6 of 6	2		ENSP00000371128.2

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

48173

AN:

109388

Hom.:

9041

Cov.:

show subpopulations

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.519

Gnomad AMR

AF:

0.421

Gnomad ASJ

AF:

0.609

Gnomad EAS

AF:

0.377

Gnomad SAS

AF:

0.563

Gnomad FIN

AF:

0.480

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.588

Gnomad OTH

AF:

0.472

GnomAD4 exome

AF:

0.560

AC:

105301

AN:

188044

Hom.:

21774

Cov.:

AF XY:

0.604

AC XY:

28907

AN XY:

47882

show subpopulations

African (AFR)

AF:

0.174

AC:

935

AN:

5362

American (AMR)

AF:

0.419

AC:

3274

AN:

7822

Ashkenazi Jewish (ASJ)

AF:

0.626

AC:

3029

AN:

4838

East Asian (EAS)

AF:

0.407

AC:

6171

AN:

15160

South Asian (SAS)

AF:

0.634

AC:

2654

AN:

4184

European-Finnish (FIN)

AF:

0.515

AC:

12084

AN:

23470

Middle Eastern (MID)

AF:

0.630

AC:

397

AN:

630

European-Non Finnish (NFE)

AF:

0.612

AC:

71140

AN:

116242

Other (OTH)

AF:

0.543

AC:

5617

AN:

10336

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

1567

3134

4701

6268

7835

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

842

1684

2526

3368

4210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.440

AC:

48174

AN:

109419

Hom.:

9041

Cov.:

AF XY:

0.427

AC XY:

13615

AN XY:

31879

show subpopulations

African (AFR)

AF:

0.163

AC:

4971

AN:

30426

American (AMR)

AF:

0.422

AC:

4311

AN:

10218

Ashkenazi Jewish (ASJ)

AF:

0.609

AC:

1597

AN:

2624

East Asian (EAS)

AF:

0.378

AC:

1303

AN:

3448

South Asian (SAS)

AF:

0.562

AC:

1450

AN:

2579

European-Finnish (FIN)

AF:

0.480

AC:

2613

AN:

5444

Middle Eastern (MID)

AF:

0.578

AC:

122

AN:

211

European-Non Finnish (NFE)

AF:

0.588

AC:

30764

AN:

52338

Other (OTH)

AF:

0.477

AC:

711

AN:

1491

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

858

1716

2574

3432

4290

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

452

904

1356

1808

2260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.467

Hom.:

6710

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.32

(source)

DANN

Benign

0.25

PhyloP100

0.34

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over