3-184711769-T-TC

Position:

• chr3-184711769-T-TC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_022149.5(MAGEF1):​c.52_53insG​(p.Glu18GlyfsTer7) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00722 in 1,521,082 control chromosomes in the GnomAD database, including 48 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0045 (2 hom., cov: 33)
  • Exomes 𝑓: 0.0075 (46 hom.)
• Consequence: MAGEF1 NM_022149.5 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.783

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 3-184711769-T-TC is Benign according to our data. Variant chr3-184711769-T-TC is described in ClinVar as [Benign]. Clinvar id is 774609.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEF1	NM_022149.5	c.52_53insG	p.Glu18GlyfsTer7	frameshift_variant	1/1	ENST00000317897.5	NP_071432.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGEF1	ENST00000317897.5	c.52_53insG	p.Glu18GlyfsTer7	frameshift_variant	1/1		NM_022149.5	ENSP00000315064	P1

Frequencies

GnomAD3 genomes AF: 0.00450 AC: 685 AN: 152124 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.00157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00242

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000620

Gnomad FIN AF: 0.00914

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00700

Gnomad OTH AF: 0.00191

GnomAD3 exomes AF: 0.00552 AC: 894 AN: 162094 Hom.: 6 AF XY: 0.00571 AC XY: 498 AN XY: 87208

Gnomad AFR exome AF: 0.00162

Gnomad AMR exome AF: 0.00183

Gnomad ASJ exome AF: 0.000316

Gnomad EAS exome AF: 0.0000659

Gnomad SAS exome AF: 0.00121

Gnomad FIN exome AF: 0.0111

Gnomad NFE exome AF: 0.00812

Gnomad OTH exome AF: 0.00541

GnomAD4 exome AF: 0.00752 AC: 10298 AN: 1368840 Hom.: 46 Cov.: 39 AF XY: 0.00724 AC XY: 4864 AN XY: 672264

Gnomad4 AFR exome AF: 0.00103

Gnomad4 AMR exome AF: 0.00181

Gnomad4 ASJ exome AF: 0.000806

Gnomad4 EAS exome AF: 0.0000513

Gnomad4 SAS exome AF: 0.00216

Gnomad4 FIN exome AF: 0.0106

Gnomad4 NFE exome AF: 0.00860

Gnomad4 OTH exome AF: 0.00560

GnomAD4 genome AF: 0.00450 AC: 685 AN: 152242 Hom.: 2 Cov.: 33 AF XY: 0.00438 AC XY: 326 AN XY: 74444

Gnomad4 AFR AF: 0.00156

Gnomad4 AMR AF: 0.00242

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000621

Gnomad4 FIN AF: 0.00914

Gnomad4 NFE AF: 0.00700

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.00681 Hom.: 1

Bravo AF: 0.00406

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 19, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs544302047; hg19: chr3-184429557;