5-42800706-C-T

Variant names:

• chr5-42800706-C-T
• rs7579
• NM_005410.4:c.*14G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005410.4(SELENOP):​c.*14G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,579,408 control chromosomes in the GnomAD database, including 69,443 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 0.26 (5715 hom., cov: 32)
  • Exomes 𝑓: 0.29 (63728 hom.)
• Consequence: SELENOP NM_005410.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

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]

CCDC152 (HGNC:34438): (coiled-coil domain containing 152)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELENOP	NM_005410.4	c.*14G>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000514985.6	NP_005401.3
CCDC152	NM_001134848.2	c.*925C>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000361970.10	NP_001128320.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELENOP	ENST00000514985	c.*14G>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_005410.4	ENSP00000420939.1
CCDC152	ENST00000361970.10	c.*925C>T		3_prime_UTR_variant	Exon 9 of 9	1	NM_001134848.2	ENSP00000354888.5

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39402 AN: 151954 Hom.: 5705 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.251

GnomAD2 exomes AF: 0.306 AC: 70631 AN: 231178 AF XY: 0.297

Gnomad AFR exome AF: 0.136

Gnomad AMR exome AF: 0.498

Gnomad ASJ exome AF: 0.284

Gnomad EAS exome AF: 0.263

Gnomad FIN exome AF: 0.346

Gnomad NFE exome AF: 0.294

Gnomad OTH exome AF: 0.280

GnomAD4 exome AF: 0.294 AC: 419522 AN: 1427336 Hom.: 63728 Cov.: 32 AF XY: 0.292 AC XY: 205646 AN XY: 705358

Gnomad4 AFR exome AF: 0.135 AC: 4361 AN: 32332

Gnomad4 AMR exome AF: 0.478 AC: 19574 AN: 40918

Gnomad4 ASJ exome AF: 0.286 AC: 7106 AN: 24886

Gnomad4 EAS exome AF: 0.320 AC: 12509 AN: 39100

Gnomad4 SAS exome AF: 0.236 AC: 19154 AN: 81316

Gnomad4 FIN exome AF: 0.345 AC: 18128 AN: 52522

Gnomad4 NFE exome AF: 0.294 AC: 321400 AN: 1091768

Gnomad4 Remaining exome AF: 0.271 AC: 15967 AN: 58876

GnomAD4 genome AF: 0.259 AC: 39444 AN: 152072 Hom.: 5715 Cov.: 32 AF XY: 0.262 AC XY: 19464 AN XY: 74330

Gnomad4 AFR AF: 0.140 AC: 0.140342 AN: 0.140342

Gnomad4 AMR AF: 0.380 AC: 0.37989 AN: 0.37989

Gnomad4 ASJ AF: 0.281 AC: 0.28053 AN: 0.28053

Gnomad4 EAS AF: 0.280 AC: 0.280247 AN: 0.280247

Gnomad4 SAS AF: 0.227 AC: 0.226517 AN: 0.226517

Gnomad4 FIN AF: 0.348 AC: 0.348098 AN: 0.348098

Gnomad4 NFE AF: 0.291 AC: 0.291065 AN: 0.291065

Gnomad4 OTH AF: 0.256 AC: 0.256167 AN: 0.256167

Alfa AF: 0.282 Hom.: 9563

Bravo AF: 0.256

Asia WGS AF: 0.240 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7579; hg19: chr5-42800808; COSMIC: COSV62792213; COSMIC: COSV62792213;