Variant rs176024 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_138702.1(MAGEC3):c.919G>A(p.Ala307Thr) variant causes a missense 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.87 ( 29987 hom., 26526 hem., cov: 21)

Exomes 𝑓: 0.91 ( 312362 hom. 327986 hem. )

Failed GnomAD Quality Control

Consequence

MAGEC3
NM_138702.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.89

Variant links:

Genes affected

MAGEC3 (HGNC:23798): (MAGE family member C3) This gene is a member of the MAGEC gene family. The members of this family are not expressed in normal tissues, except for testis, and are expressed in tumors of various histological types. The MAGEC genes are clustered on chromosome Xq26-q27. Two transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MAGEC3 links:

MAGEC3 (HGNC:):

MAGEC3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEC3	NM_138702.1 linkuse as main transcript	c.919G>A	p.Ala307Thr	missense_variant	5/8	ENST00000298296.1	NP_619647.1	Q8TD91-1
MAGEC3	NM_177456.2 linkuse as main transcript	c.-369G>A		5_prime_UTR_variant	2/5		NP_803251.1	Q8TD91-2
MAGEC3	XM_011531267.4 linkuse as main transcript	c.-292G>A		upstream_gene_variant			XP_011529569.1	Q8TD91-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MAGEC3	ENST00000298296.1 linkuse as main transcript	c.919G>A	p.Ala307Thr	missense_variant	5/8	1	NM_138702.1	ENSP00000298296.1	Q8TD91-1
MAGEC3	ENST00000443323.2 linkuse as main transcript	c.-118-1153G>A		intron_variant		1		ENSP00000438254.1	Q3SYA6
MAGEC3	ENST00000544766 linkuse as main transcript	c.-369G>A		5_prime_UTR_variant	2/5	5		ENSP00000440444.1	Q8TD91-2
MAGEC3	ENST00000483584.5 linkuse as main transcript	n.159G>A		non_coding_transcript_exon_variant	2/5	5

Frequencies

GnomAD3 genomes

AF:

0.867

AC:

94184

AN:

108690

Hom.:

30002

Cov.:

AF XY:

0.852

AC XY:

26488

AN XY:

31072

show subpopulations

Gnomad AFR

AF:

0.802

Gnomad AMI

AF:

0.951

Gnomad AMR

AF:

0.770

Gnomad ASJ

AF:

0.945

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.648

Gnomad FIN

AF:

0.905

Gnomad MID

AF:

0.902

Gnomad NFE

AF:

0.949

Gnomad OTH

AF:

0.856

GnomAD3 exomes

AF:

0.837

AC:

152717

AN:

182357

Hom.:

41786

AF XY:

0.837

AC XY:

56032

AN XY:

66913

show subpopulations

Gnomad AFR exome

AF:

0.804

Gnomad AMR exome

AF:

0.736

Gnomad ASJ exome

AF:

0.949

Gnomad EAS exome

AF:

0.476

Gnomad SAS exome

AF:

0.671

Gnomad FIN exome

AF:

0.912

Gnomad NFE exome

AF:

0.950

Gnomad OTH exome

AF:

0.877

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.912

AC:

1001001

AN:

1097164

Hom.:

312362

Cov.:

AF XY:

0.904

AC XY:

327986

AN XY:

362648

show subpopulations

Gnomad4 AFR exome

AF:

0.801

Gnomad4 AMR exome

AF:

0.745

Gnomad4 ASJ exome

AF:

0.952

Gnomad4 EAS exome

AF:

0.484

Gnomad4 SAS exome

AF:

0.677

Gnomad4 FIN exome

AF:

0.917

Gnomad4 NFE exome

AF:

0.954

Gnomad4 OTH exome

AF:

0.883

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.866

AC:

94195

AN:

108733

Hom.:

29987

Cov.:

AF XY:

0.852

AC XY:

26526

AN XY:

31125

show subpopulations

Gnomad4 AFR

AF:

0.802

Gnomad4 AMR

AF:

0.769

Gnomad4 ASJ

AF:

0.945

Gnomad4 EAS

AF:

0.470

Gnomad4 SAS

AF:

0.649

Gnomad4 FIN

AF:

0.905

Gnomad4 NFE

AF:

0.949

Gnomad4 OTH

AF:

0.848

Alfa

AF:

0.925

Hom.:

134332

Bravo

AF:

0.855

TwinsUK

AF:

0.954

AC:

3536

ALSPAC

AF:

0.957

AC:

2764

ESP6500AA

AF:

0.808

AC:

3099

ESP6500EA

AF:

0.952

AC:

6404

ExAC

AF:

0.840

AC:

101989

EpiCase

AF:

0.951

EpiControl

AF:

0.948

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.072

BayesDel_addAF

Benign

-1.0

BayesDel_noAF

Benign

-1.1

CADD

Benign

DANN

Benign

0.31

DEOGEN2

Benign

0.015

FATHMM_MKL

Benign

0.00086

LIST_S2

Benign

0.23

MetaRNN

Benign

0.0000026

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.51

PrimateAI

Uncertain

0.56

PROVEAN

Benign

0.16

REVEL

Benign

0.015

Sift

Benign

0.21

Sift4G

Benign

0.15

Polyphen

0.0010

Vest4

0.035

MPC

0.020

ClinPred

0.0029

GERP RS

0.0071

Varity_R

0.035

gMVP

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.78

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.78

Position offset: 10

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over