rs34995413

Positions:

• chr3-184711345-ATCCTCCTCCTCC-A
• chr3-184711345-ATCCTCCTCCTCC-ATCC
• chr3-184711345-ATCCTCCTCCTCC-ATCCTCC
• chr3-184711345-ATCCTCCTCCTCC-ATCCTCCTCC
• chr3-184711345-ATCCTCCTCCTCC-ATCCTCCTCCTCCTCC
• chr3-184711345-ATCCTCCTCCTCC-ATCCTCCTCCTCCTCCTCC
• chr3-184711345-ATCCTCCTCCTCC-ATCCTCCTCCTCCTCCTCCTCC
• chr3-184711345-ATCCTCCTCCTCC-ATCCTCCTCCTCCTCCTCCTCCTCC
• chr3-184711345-ATCCTCCTCCTCC-ATCCTCCTCCTCCTCCTCCTCCTCCTCC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_022149.5(MAGEF1):​c.465_476delGGAGGAGGAGGA​(p.Glu155_Glu158del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000191 in 1,567,480 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: MAGEF1 NM_022149.5 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

Genes affected

MAGEF1 (HGNC:29639): (MAGE family member F1) This intronless gene encodes a member of the MAGE superfamily. It is ubiquitously expressed in normal tissues and in tumor cells. This gene includes a microsatellite repeat in the coding region. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEF1	NM_022149.5	c.465_476delGGAGGAGGAGGA	p.Glu155_Glu158del	disruptive_inframe_deletion	1/1	ENST00000317897.5	NP_071432.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGEF1	ENST00000317897.5	c.465_476delGGAGGAGGAGGA	p.Glu155_Glu158del	disruptive_inframe_deletion	1/1	6	NM_022149.5	ENSP00000315064.3

Frequencies

GnomAD3 genomes AF: 0.00000665 AC: 1 AN: 150448 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

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: 0.0000148

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000141 AC: 2 AN: 1417032 Hom.: 0 AF XY: 0.00000142 AC XY: 1 AN XY: 705690

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000186

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000665 AC: 1 AN: 150448 Hom.: 0 Cov.: 0 AF XY: 0.0000136 AC XY: 1 AN XY: 73408

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000148

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34995413; hg19: chr3-184429133;