1-151372265-T-G

Variant names:

• chr1-151372265-T-G
• rs2769264
• NM_003944.4:c.4+373A>C

Variant summary

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

The ENST00000368868.10(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 ENST00000368868.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 36 publications found

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]

SELENBP1 Gene-Disease associations (from GenCC):

• extraoral halitosis due to methanethiol oxidase deficiency

  Inheritance: AR Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, ClinGen
• autosomal recessive extra-oral halitosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368868.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELENBP1	NM_003944.4	MANE Select	c.4+373A>C		intron	N/A	NP_003935.2
	SELENBP1	NM_001258289.2		c.-80+373A>C		intron	N/A	NP_001245218.1
	SELENBP1	NM_001258288.2		c.4+373A>C		intron	N/A	NP_001245217.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELENBP1	ENST00000368868.10	TSL:1 MANE Select	c.4+373A>C		intron	N/A	ENSP00000357861.5
	SELENBP1	ENST00000426705.6	TSL:2	c.-80+373A>C		intron	N/A	ENSP00000397261.2
	SELENBP1	ENST00000447402.7	TSL:2	c.4+373A>C		intron	N/A	ENSP00000413960.3

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

African (AFR) AF: 0.316 AC: 13085 AN: 41438

American (AMR) AF: 0.299 AC: 4571 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1552 AN: 5152

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4822

European-Finnish (FIN) AF: 0.167 AC: 1771 AN: 10590

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12131 AN: 67970

Other (OTH) AF: 0.212 AC: 449 AN: 2116

Alfa AF: 0.205 Hom.: 8212

Bravo AF: 0.251

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.1
DANN	Benign	0.52
PhyloP100		0.15
PromoterAI		0.029	Neutral
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

Other links and lift over

dbSNP: rs2769264; hg19: chr1-151344741;