Variant 16-56403084-A-AGGCT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5

The NM_001144.6(AMFR):c.874_875insAGCC(p.Leu292GlnfsTer14) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)

Consequence

AMFR
NM_001144.6 frameshift

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 0.642

Variant links:

Genes affected

AMFR (HGNC:463): (autocrine motility factor receptor) This locus encodes a glycosylated transmembrane receptor. Its ligand, autocrine motility factor, is a tumor motility-stimulating protein secreted by tumor cells. The encoded receptor is also a member of the E3 ubiquitin ligase family of proteins. It catalyzes ubiquitination and endoplasmic reticulum-associated degradation of specific proteins. [provided by RefSeq, Feb 2012]

AMFR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 16-56403084-A-AGGCT is Pathogenic according to our data. Variant chr16-56403084-A-AGGCT is described in ClinVar as [Pathogenic]. Clinvar id is 2502911.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
AMFR	NM_001144.6 linkuse as main transcript	c.874_875insAGCC	p.Leu292GlnfsTer14	frameshift_variant	7/14	ENST00000290649.10
AMFR	NM_001323511.2 linkuse as main transcript	c.589_590insAGCC	p.Leu197GlnfsTer14	frameshift_variant	7/14
AMFR	NM_001323512.2 linkuse as main transcript	c.874_875insAGCC	p.Leu292GlnfsTer14	frameshift_variant	7/15
AMFR	XM_005255890.5 linkuse as main transcript	c.589_590insAGCC	p.Leu197GlnfsTer14	frameshift_variant	7/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
AMFR	ENST00000290649.10 linkuse as main transcript	c.874_875insAGCC	p.Leu292GlnfsTer14	frameshift_variant	7/14	1	NM_001144.6	P1
AMFR	ENST00000492830.5 linkuse as main transcript	c.33_34insAGCC	p.Trp12SerfsTer85	frameshift_variant	1/7	2
AMFR	ENST00000565445.5 linkuse as main transcript	c.589_590insAGCC	p.Leu197GlnfsTer14	frameshift_variant	7/7	5
AMFR	ENST00000567738.1 linkuse as main transcript	c.19_20insAGCC	p.Leu7GlnfsTer14	frameshift_variant	1/8	5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Spastic paraplegia 89, autosomal recessive

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

May 25, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over