1-1050069-G-T

Variant names:

• chr1-1050069-G-T
• rs2799067
• NM_198576.4:c.4879+32G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_198576.4(AGRN):​c.4879+32G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 22)
  • Exomes 𝑓: 0.00013 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: AGRN NM_198576.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 0 publications found

Genes affected

AGRN (HGNC:329): (agrin) This gene encodes one of several proteins that are critical in the development of the neuromuscular junction (NMJ), as identified in mouse knock-out studies. The encoded protein contains several laminin G, Kazal type serine protease inhibitor, and epidermal growth factor domains. Additional post-translational modifications occur to add glycosaminoglycans and disulfide bonds. In one family with congenital myasthenic syndrome affecting limb-girdle muscles, a mutation in this gene was found. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2015]

AGRN Gene-Disease associations (from GenCC):

• congenital myasthenic syndrome 8

  Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• presynaptic congenital myasthenic syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• postsynaptic congenital myasthenic syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198576.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGRN	NM_198576.4	MANE Select	c.4879+32G>T		intron	N/A	NP_940978.2
	AGRN	NM_001305275.2		c.4879+32G>T		intron	N/A	NP_001292204.1
	AGRN	NM_001364727.2		c.4564+32G>T		intron	N/A	NP_001351656.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGRN	ENST00000379370.7	TSL:1 MANE Select	c.4879+32G>T		intron	N/A	ENSP00000368678.2
	AGRN	ENST00000651234.1		c.4564+32G>T		intron	N/A	ENSP00000499046.1
	AGRN	ENST00000652369.2		c.4564+32G>T		intron	N/A	ENSP00000498543.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 108406 Hom.: 0 Cov.: 22

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000131 AC: 148 AN: 1126254 Hom.: 0 Cov.: 19 AF XY: 0.000111 AC XY: 62 AN XY: 560336

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 24336

American (AMR) AF: 0.00 AC: 0 AN: 32356

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21876

East Asian (EAS) AF: 0.0000305 AC: 1 AN: 32806

South Asian (SAS) AF: 0.0000585 AC: 4 AN: 68398

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 42634

Middle Eastern (MID) AF: 0.000291 AC: 1 AN: 3436

European-Non Finnish (NFE) AF: 0.000156 AC: 133 AN: 852678

Other (OTH) AF: 0.000189 AC: 9 AN: 47734

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 108406 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 52902

African (AFR) AF: 0.00 AC: 0 AN: 20612

American (AMR) AF: 0.00 AC: 0 AN: 12002

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2832

East Asian (EAS) AF: 0.00 AC: 0 AN: 3310

South Asian (SAS) AF: 0.00 AC: 0 AN: 3754

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7982

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 270

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 55352

Other (OTH) AF: 0.00 AC: 0 AN: 1576

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.35
PhyloP100		0.17

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

Other links and lift over

dbSNP: rs2799067; hg19: chr1-985449;