rs2769264

Positions:

• chr1-151372265-T-G

Variant summary

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

The NM_003944.4(SELENBP1):​c.4+373A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,038 control chromosomes in the GnomAD database, including 4,498 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 0.23 (4498 hom., cov: 32)
• Consequence: SELENBP1 NM_003944.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

SELENBP1 (HGNC:10719): (selenium binding protein 1) This gene encodes a member of the selenium-binding protein family. Selenium is an essential nutrient that exhibits potent anticarcinogenic properties, and deficiency of selenium may cause certain neurologic diseases. The effects of selenium in preventing cancer and neurologic diseases may be mediated by selenium-binding proteins, and decreased expression of this gene may be associated with several types of cancer. The encoded protein may play a selenium-dependent role in ubiquitination/deubiquitination-mediated protein degradation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELENBP1	NM_003944.4	c.4+373A>C		intron_variant		ENST00000368868.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELENBP1	ENST00000368868.10	c.4+373A>C		intron_variant		1	NM_003944.4	P1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35358 AN: 151920 Hom.: 4486 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.233 AC: 35390 AN: 152038 Hom.: 4498 Cov.: 32 AF XY: 0.232 AC XY: 17237 AN XY: 74314

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.212

Alfa AF: 0.197 Hom.: 1981

Bravo AF: 0.251

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.1
DANN	Benign	0.52

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: rs2769264; hg19: chr1-151344741;