NM_020451.3:c.747+39C>T

Variant names:

• chr1-25808828-C-T
• rs114458946
• NM_020451.3:c.747+39C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_020451.3(SELENON):​c.747+39C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00225 in 1,610,098 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0075 (15 hom., cov: 33)
  • Exomes 𝑓: 0.0017 (17 hom.)
• Consequence: SELENON NM_020451.3 intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: 0.155
• Publications: 0 publications found

Genes affected

SELENON (HGNC:15999): (selenoprotein N) This gene encodes a glycoprotein that is localized in the endoplasmic reticulum. It plays an important role in cell protection against oxidative stress, and in the regulation of redox-related calcium homeostasis. Mutations in this gene are associated with early onset muscle disorders, referred to as SEPN1-related myopathy. SEPN1-related myopathy consists of 4 autosomal recessive disorders, originally thought to be separate entities: rigid spine muscular dystrophy (RSMD1), the classical form of multiminicore disease, desmin related myopathy with Mallory-body like inclusions, and congenital fiber-type disproportion (CFTD). This protein is a selenoprotein, containing the rare amino acid selenocysteine (Sec). Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. A second stop-codon redefinition element (SRE) adjacent to the UGA codon has been identified in this gene (PMID:15791204). SRE is a phylogenetically conserved stem-loop structure that stimulates readthrough at the UGA codon, and augments the Sec insertion efficiency by SECIS. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2016]

SELENON Gene-Disease associations (from GenCC):

• rigid spine muscular dystrophy 1

  Inheritance: AR Classification: DEFINITIVE Submitted by: Ambry Genetics, G2P
• SELENON-related myopathy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• congenital myopathy 4A, autosomal dominant

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• congenital fiber-type disproportion myopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• desmin-related myopathy with Mallory body-like inclusions

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• rigid spine syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BP6: Variant 1-25808828-C-T is Benign according to our data. Variant chr1-25808828-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 261286.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00748 (1139/152280) while in subpopulation AFR AF = 0.0223 (927/41566). AF 95% confidence interval is 0.0211. There are 15 homozygotes in GnomAd4. There are 552 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 15 AR,AD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELENON	NM_020451.3	c.747+39C>T		intron_variant	Intron 5 of 12	ENST00000361547.7	NP_065184.2
SELENON	NM_206926.2	c.645+39C>T		intron_variant	Intron 4 of 11		NP_996809.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELENON	ENST00000361547.7	c.747+39C>T		intron_variant	Intron 5 of 12	1	NM_020451.3	ENSP00000355141.2
SELENON	ENST00000374315.1	c.645+39C>T		intron_variant	Intron 4 of 11	5		ENSP00000363434.1
SELENON	ENST00000354177.9	c.645+39C>T		intron_variant	Intron 4 of 11	5		ENSP00000346109.5
SELENON	ENST00000494537.2	n.645+39C>T		intron_variant	Intron 4 of 12	3		ENSP00000508308.1

Frequencies

GnomAD3 genomes AF: 0.00745 AC: 1133 AN: 152162 Hom.: 15 Cov.: 33

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00380

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.00393

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000588

Gnomad OTH AF: 0.00382

GnomAD2 exomes AF: 0.00398 AC: 982 AN: 246530 AF XY: 0.00369

Gnomad AFR exome AF: 0.0229

Gnomad AMR exome AF: 0.00166

Gnomad ASJ exome AF: 0.00471

Gnomad EAS exome AF: 0.0125

Gnomad FIN exome AF: 0.00168

Gnomad NFE exome AF: 0.000928

Gnomad OTH exome AF: 0.00200

GnomAD4 exome AF: 0.00170 AC: 2478 AN: 1457818 Hom.: 17 Cov.: 31 AF XY: 0.00171 AC XY: 1244 AN XY: 725426

African (AFR) AF: 0.0218 AC: 728 AN: 33428

American (AMR) AF: 0.00168 AC: 75 AN: 44682

Ashkenazi Jewish (ASJ) AF: 0.00395 AC: 103 AN: 26094

East Asian (EAS) AF: 0.0101 AC: 402 AN: 39670

South Asian (SAS) AF: 0.00492 AC: 424 AN: 86150

European-Finnish (FIN) AF: 0.00184 AC: 97 AN: 52686

Middle Eastern (MID) AF: 0.00208 AC: 12 AN: 5760

European-Non Finnish (NFE) AF: 0.000414 AC: 459 AN: 1109108

Other (OTH) AF: 0.00295 AC: 178 AN: 60240

GnomAD4 genome AF: 0.00748 AC: 1139 AN: 152280 Hom.: 15 Cov.: 33 AF XY: 0.00742 AC XY: 552 AN XY: 74442

African (AFR) AF: 0.0223 AC: 927 AN: 41566

American (AMR) AF: 0.00379 AC: 58 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3472

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5186

South Asian (SAS) AF: 0.00393 AC: 19 AN: 4830

European-Finnish (FIN) AF: 0.00170 AC: 18 AN: 10614

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000588 AC: 40 AN: 67992

Other (OTH) AF: 0.00378 AC: 8 AN: 2114

Alfa AF: 0.00180 Hom.: 0

Bravo AF: 0.00857

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Feb 10, 2017

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:2

Aug 14, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	6.1
DANN	Benign	0.86
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism

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: rs114458946; hg19: chr1-26135319;