rs2972756

Positions:

• chr5-42820023-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506577.5(SELENOP):​c.-14+5418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,998 control chromosomes in the GnomAD database, including 24,827 homozygotes. 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 0.57 (24827 hom., cov: 31)
• Consequence: SELENOP ENST00000506577.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

Genes affected

SELENOP (HGNC:10751): (selenoprotein P) This gene encodes a selenoprotein that is predominantly expressed in the liver and secreted into the plasma. This selenoprotein is unique in that it contains multiple selenocysteine (Sec) residues per polypeptide (10 in human), and accounts for most of the selenium in plasma. It has been implicated as an extracellular antioxidant, and in the transport of selenium to extra-hepatic tissues via apolipoprotein E receptor-2 (apoER2). Mice lacking this gene exhibit neurological dysfunction, suggesting its importance in normal brain function. 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. The mRNA for this selenoprotein contains two SECIS elements. The use of alternative polyadenylation sites, one located in between the two SECIS elements, results in two populations of mRNAs containing either both (predominant) or just the upstream SECIS element (PMID:27881738). Alternatively spliced transcript variants have also been found for this gene. [provided by RefSeq, Oct 2018]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42820023A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELENOP	ENST00000506577.5	c.-14+5418T>C		intron_variant		1		ENSP00000425915.1
SELENOP	ENST00000514218.5	c.-13-11657T>C		intron_variant		5		ENSP00000421626.1
ENSG00000286271	ENST00000651306.1	n.377+2672A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86323 AN: 151880 Hom.: 24781 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.560

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.569 AC: 86440 AN: 151998 Hom.: 24827 Cov.: 31 AF XY: 0.568 AC XY: 42209 AN XY: 74308

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.563

Alfa AF: 0.569 Hom.: 32861

Bravo AF: 0.563

Asia WGS AF: 0.466 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2972756; hg19: chr5-42820125;