1-1046562-C-A

Position:

chr1-1046562-C-A

Variant summary

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

The NM_198576.4(AGRN):c.3077C>A(p.Thr1026Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00596 in 1,609,174 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0070 ( 14 hom., cov: 33)

Exomes 𝑓: 0.0058 ( 52 hom. )

Consequence

AGRN
NM_198576.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.30

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 (MetaRNN=0.0045595467).

BP6

Variant 1-1046562-C-A is Benign according to our data. Variant chr1-1046562-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 263179.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00703 (1070/152272) while in subpopulation EAS AF= 0.0325 (168/5172). AF 95% confidence interval is 0.0285. There are 14 homozygotes in gnomad4. There are 606 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGRN	NM_198576.4 linkuse as main transcript	c.3077C>A	p.Thr1026Asn	missense_variant	18/36	ENST00000379370.7	NP_940978.2	O00468-6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
AGRN	ENST00000379370.7 linkuse as main transcript	c.3077C>A	p.Thr1026Asn	missense_variant	18/36	1	NM_198576.4	ENSP00000368678.2	O00468-6
AGRN	ENST00000651234.1 linkuse as main transcript	c.2762C>A	p.Thr921Asn	missense_variant	17/38			ENSP00000499046.1	A0A494C1I6
AGRN	ENST00000652369.1 linkuse as main transcript	c.2762C>A	p.Thr921Asn	missense_variant	17/35			ENSP00000498543.1	A0A494C0G5
AGRN	ENST00000620552.4 linkuse as main transcript	c.2663C>A	p.Thr888Asn	missense_variant	18/39	5		ENSP00000484607.1	A0A087X208

Frequencies

GnomAD3 genomes

AF:

0.00703

AC:

1070

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000724

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.00589

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.0326

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.0285

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00626

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.00811

AC:

1972

AN:

243190

Hom.:

AF XY:

0.00790

AC XY:

1049

AN XY:

132858

show subpopulations

Gnomad AFR exome

AF:

0.000579

Gnomad AMR exome

AF:

0.00108

Gnomad ASJ exome

AF:

0.00131

Gnomad EAS exome

AF:

0.0330

Gnomad SAS exome

AF:

0.00243

Gnomad FIN exome

AF:

0.0267

Gnomad NFE exome

AF:

0.00621

Gnomad OTH exome

AF:

0.00920

GnomAD4 exome

AF:

0.00584

AC:

8514

AN:

1456902

Hom.:

Cov.:

AF XY:

0.00583

AC XY:

4223

AN XY:

724898

show subpopulations

Gnomad4 AFR exome

AF:

0.000538

Gnomad4 AMR exome

AF:

0.00164

Gnomad4 ASJ exome

AF:

0.00207

Gnomad4 EAS exome

AF:

0.0293

Gnomad4 SAS exome

AF:

0.00247

Gnomad4 FIN exome

AF:

0.0263

Gnomad4 NFE exome

AF:

0.00479

Gnomad4 OTH exome

AF:

0.00589

GnomAD4 genome

AF:

0.00703

AC:

1070

AN:

152272

Hom.:

Cov.:

AF XY:

0.00814

AC XY:

606

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.000722

Gnomad4 AMR

AF:

0.00588

Gnomad4 ASJ

AF:

0.00230

Gnomad4 EAS

AF:

0.0325

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.0285

Gnomad4 NFE

AF:

0.00626

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00637

Hom.:

Bravo

AF:

0.00511

TwinsUK

AF:

0.00189

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00419

AC:

ExAC

AF:

0.00844

AC:

1018

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.00431

EpiControl

AF:

0.00528

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Feb 23, 2017	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Congenital myasthenic syndrome 8

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 24, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Benign

0.95

Eigen

Benign

0.12

Eigen_PC

Benign

0.012

FATHMM_MKL

Benign

0.54

LIST_S2

Benign

0.82

T;T

MetaRNN

Benign

0.0046

T;T

MetaSVM

Benign

-0.76

MutationAssessor

Uncertain

2.1

M;.

PrimateAI

Benign

0.41

PROVEAN

Benign

-1.6

N;.

REVEL

Benign

0.17

Sift

Benign

0.29

T;.

Sift4G

Benign

0.088

T;T

Vest4

0.27

MVP

0.84

MPC

0.29

ClinPred

0.012

GERP RS

4.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

gMVP

0.21

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

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