NM_198576.4:c.4977-10A>G

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_198576.4(AGRN):c.4977-10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0257 in 1,612,724 control chromosomes in the GnomAD database, including 655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 51 hom., cov: 33)

Exomes 𝑓: 0.026 ( 604 hom. )

Consequence

AGRN
NM_198576.4 intron

Scores

Splicing: ADA: 0.00002238

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.27

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 1-1050417-A-G is Benign according to our data. Variant chr1-1050417-A-G is described in ClinVar as [Benign]. Clinvar id is 263193.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-1050417-A-G is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0185 (2807/152140) while in subpopulation NFE AF= 0.0304 (2068/67924). AF 95% confidence interval is 0.0294. There are 51 homozygotes in gnomad4. There are 1299 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 51 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGRN	NM_198576.4 link	c.4977-10A>G		intron_variant	Intron 28 of 35	ENST00000379370.7	NP_940978.2	O00468-6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
AGRN	ENST00000379370.7 link	c.4977-10A>G	intron_variant	Intron 28 of 35	1	NM_198576.4	ENSP00000368678.2	O00468-6
AGRN	ENST00000651234.1 link	c.4662-10A>G	intron_variant	Intron 27 of 37			ENSP00000499046.1	A0A494C1I6
AGRN	ENST00000652369.1 link	c.4662-10A>G	intron_variant	Intron 27 of 34			ENSP00000498543.1	A0A494C0G5
AGRN	ENST00000620552.4 link	c.4563-10A>G	intron_variant	Intron 28 of 38	5		ENSP00000484607.1	A0A087X208

Frequencies

GnomAD3 genomes

AF:

0.0185

AC:

2812

AN:

152022

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00464

Gnomad AMI

AF:

0.0736

Gnomad AMR

AF:

0.0117

Gnomad ASJ

AF:

0.0158

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0244

Gnomad FIN

AF:

0.00923

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0304

Gnomad OTH

AF:

0.0125

GnomAD3 exomes

AF:

0.0184

AC:

4542

AN:

247310

Hom.:

AF XY:

0.0191

AC XY:

2576

AN XY:

134618

show subpopulations

Gnomad AFR exome

AF:

0.00468

Gnomad AMR exome

AF:

0.00834

Gnomad ASJ exome

AF:

0.0169

Gnomad EAS exome

AF:

0.0000553

Gnomad SAS exome

AF:

0.0194

Gnomad FIN exome

AF:

0.00979

Gnomad NFE exome

AF:

0.0278

Gnomad OTH exome

AF:

0.0197

GnomAD4 exome

AF:

0.0265

AC:

38659

AN:

1460584

Hom.:

604

Cov.:

AF XY:

0.0265

AC XY:

19230

AN XY:

726614

show subpopulations

Gnomad4 AFR exome

AF:

0.00373

Gnomad4 AMR exome

AF:

0.00862

Gnomad4 ASJ exome

AF:

0.0183

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0207

Gnomad4 FIN exome

AF:

0.00934

Gnomad4 NFE exome

AF:

0.0304

Gnomad4 OTH exome

AF:

0.0247

GnomAD4 genome

AF:

0.0185

AC:

2807

AN:

152140

Hom.:

Cov.:

AF XY:

0.0175

AC XY:

1299

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.00462

Gnomad4 AMR

AF:

0.0116

Gnomad4 ASJ

AF:

0.0158

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0242

Gnomad4 FIN

AF:

0.00923

Gnomad4 NFE

AF:

0.0304

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.0233

Hom.:

Bravo

AF:

0.0173

Asia WGS

AF:

0.00549

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Jun 21, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Nov 06, 2020

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Congenital myasthenic syndrome 8

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.86

DANN

Benign

0.45

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000022

dbscSNV1_RF

Benign

0.0040

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over