Variant X-141895317-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_138702.1(MAGEC3):c.958C>T(p.Leu320=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,207,295 control chromosomes in the GnomAD database, including 29,650 homozygotes. There are 97,156 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 0.29 ( 3870 hom., 8435 hem., cov: 21)

Exomes 𝑓: 0.25 ( 25780 hom. 88721 hem. )

Consequence

MAGEC3
NM_138702.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

BP7

Synonymous conserved (PhyloP=-2.18 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
MAGEC3	NM_138702.1 linkuse as main transcript	c.958C>T	p.Leu320=	synonymous_variant	5/8	ENST00000298296.1	NP_619647.1
MAGEC3	NM_177456.2 linkuse as main transcript	c.-330C>T		5_prime_UTR_variant	2/5		NP_803251.1
MAGEC3	XM_011531267.4 linkuse as main transcript	c.-253C>T		5_prime_UTR_variant	1/3		XP_011529569.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGEC3	ENST00000298296.1 linkuse as main transcript	c.958C>T	p.Leu320=	synonymous_variant	5/8	1	NM_138702.1	ENSP00000298296	P2	Q8TD91-1
MAGEC3	ENST00000443323.2 linkuse as main transcript	c.-118-1114C>T		intron_variant		1		ENSP00000438254	A2
MAGEC3	ENST00000544766.5 linkuse as main transcript	c.-330C>T		5_prime_UTR_variant	2/5	5		ENSP00000440444	A2	Q8TD91-2
MAGEC3	ENST00000483584.5 linkuse as main transcript	n.198C>T		non_coding_transcript_exon_variant	2/5	5

Frequencies

GnomAD3 genomes

AF:

0.289

AC:

31594

AN:

109437

Hom.:

3870

Cov.:

AF XY:

0.264

AC XY:

8411

AN XY:

31805

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.0484

Gnomad SAS

AF:

0.0783

Gnomad FIN

AF:

0.190

Gnomad MID

AF:

0.312

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.281

GnomAD3 exomes

AF:

0.222

AC:

40612

AN:

183234

Hom.:

3631

AF XY:

0.213

AC XY:

14435

AN XY:

67702

show subpopulations

Gnomad AFR exome

AF:

0.452

Gnomad AMR exome

AF:

0.153

Gnomad ASJ exome

AF:

0.328

Gnomad EAS exome

AF:

0.0511

Gnomad SAS exome

AF:

0.0842

Gnomad FIN exome

AF:

0.200

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.243

GnomAD4 exome

AF:

0.252

AC:

276128

AN:

1097814

Hom.:

25780

Cov.:

AF XY:

0.244

AC XY:

88721

AN XY:

363238

show subpopulations

Gnomad4 AFR exome

AF:

0.446

Gnomad4 AMR exome

AF:

0.162

Gnomad4 ASJ exome

AF:

0.324

Gnomad4 EAS exome

AF:

0.0446

Gnomad4 SAS exome

AF:

0.0908

Gnomad4 FIN exome

AF:

0.201

Gnomad4 NFE exome

AF:

0.268

Gnomad4 OTH exome

AF:

0.256

GnomAD4 genome

AF:

0.289

AC:

31605

AN:

109481

Hom.:

3870

Cov.:

AF XY:

0.265

AC XY:

8435

AN XY:

31859

show subpopulations

Gnomad4 AFR

AF:

0.435

Gnomad4 AMR

AF:

0.212

Gnomad4 ASJ

AF:

0.312

Gnomad4 EAS

AF:

0.0483

Gnomad4 SAS

AF:

0.0778

Gnomad4 FIN

AF:

0.190

Gnomad4 NFE

AF:

0.258

Gnomad4 OTH

AF:

0.277

Alfa

AF:

0.274

Hom.:

2525

Bravo

AF:

0.302

EpiCase

AF:

0.268

EpiControl

AF:

0.264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.35

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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

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