chr3-49718209-C-CCAGCGGCGG

Variant names:

• chr3-49718209-C-CCAGCGGCGG
• rs543098573
• NM_198722.3:c.1248_1256dupCCGCCGCTG

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP3 BP6_Moderate BS2

The NM_198722.3(AMIGO3):​c.1248_1256dupCCGCCGCTG​(p.Cys416_Arg418dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,612,336 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0041 (2 hom., cov: 33)
  • Exomes 𝑓: 0.0011 (6 hom.)
• Consequence: AMIGO3 NM_198722.3 disruptive_inframe_insertion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.518
• Publications: 0 publications found

Genes affected

AMIGO3 (HGNC:24075): (adhesion molecule with Ig like domain 3) Predicted to be involved in brain development and heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules. Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

RNF123 (HGNC:21148): (ring finger protein 123) The protein encoded by this gene contains a C-terminal RING finger domain, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions, and an N-terminal SPRY domain. This protein displays E3 ubiquitin ligase activity toward the cyclin-dependent kinase inhibitor 1B which is also known as p27 or KIP1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

GMPPB (HGNC:22932): (GDP-mannose pyrophosphorylase B) This gene is thought to encode a GDP-mannose pyrophosphorylase. The encoded protein catalyzes the conversion of mannose-1-phosphate and GTP to GDP-mannose, a reaction involved in the production of N-linked oligosaccharides. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jan 2009]

GMPPB Gene-Disease associations (from GenCC):

• muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
• myopathy caused by variation in GMPPB

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• autosomal recessive limb-girdle muscular dystrophy type 2T

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)
• congenital myasthenic syndrome

  Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp
• congenital muscular dystrophy with cerebellar involvement

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• congenital muscular dystrophy with intellectual disability

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• congenital myasthenic syndromes with glycosylation defect

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• muscle-eye-brain disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_198722.3
• BP6: Variant 3-49718209-C-CCAGCGGCGG is Benign according to our data. Variant chr3-49718209-C-CCAGCGGCGG is described in ClinVar as Benign. ClinVar VariationId is 2653845.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198722.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMIGO3	NM_198722.3	MANE Select	c.1248_1256dupCCGCCGCTG	p.Cys416_Arg418dup	disruptive_inframe_insertion	Exon 1 of 1	NP_942015.1	Q86WK7
	RNF123	NM_022064.5	MANE Select	c.3500+1740_3500+1748dupGGCAGCGGC		intron	N/A	NP_071347.2
	RNF123	NR_135218.2		n.3826+1740_3826+1748dupGGCAGCGGC		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMIGO3	ENST00000320431.8	TSL:6 MANE Select	c.1248_1256dupCCGCCGCTG	p.Cys416_Arg418dup	disruptive_inframe_insertion	Exon 1 of 1	ENSP00000323096.7	Q86WK7
	RNF123	ENST00000327697.11	TSL:1 MANE Select	c.3500+1740_3500+1748dupGGCAGCGGC		intron	N/A	ENSP00000328287.6	Q5XPI4-1
	RNF123	ENST00000457726.5	TSL:1	n.*1574+1740_*1574+1748dupGGCAGCGGC		intron	N/A	ENSP00000394369.1	C9JS59

Frequencies

GnomAD3 genomes AF: 0.00410 AC: 624 AN: 152156 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.0130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00137

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000823

Gnomad OTH AF: 0.00334

GnomAD2 exomes AF: 0.00109 AC: 268 AN: 245970 AF XY: 0.000904

Gnomad AFR exome AF: 0.0122

Gnomad AMR exome AF: 0.000666

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000464

Gnomad NFE exome AF: 0.000475

Gnomad OTH exome AF: 0.000165

GnomAD4 exome AF: 0.00107 AC: 1555 AN: 1460064 Hom.: 6 Cov.: 31 AF XY: 0.000983 AC XY: 714 AN XY: 726320

African (AFR) AF: 0.0149 AC: 498 AN: 33464

American (AMR) AF: 0.000716 AC: 32 AN: 44684

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26094

East Asian (EAS) AF: 0.00 AC: 0 AN: 39658

South Asian (SAS) AF: 0.000116 AC: 10 AN: 86226

European-Finnish (FIN) AF: 0.0000383 AC: 2 AN: 52270

Middle Eastern (MID) AF: 0.00191 AC: 11 AN: 5764

European-Non Finnish (NFE) AF: 0.000780 AC: 867 AN: 1111550

Other (OTH) AF: 0.00224 AC: 135 AN: 60354

GnomAD4 genome AF: 0.00410 AC: 624 AN: 152272 Hom.: 2 Cov.: 33 AF XY: 0.00398 AC XY: 296 AN XY: 74452

African (AFR) AF: 0.0130 AC: 539 AN: 41566

American (AMR) AF: 0.00137 AC: 21 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000823 AC: 56 AN: 68006

Other (OTH) AF: 0.00331 AC: 7 AN: 2116

Alfa AF: 0.000610 Hom.: 0

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.52
Mutation Taster		=80/20	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs543098573; hg19: chr3-49755642;