1-151365312-A-G

Variant names:

• chr1-151365312-A-G
• rs10788804
• NM_003944.4:c.1045-31T>C

Variant summary

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

The ENST00000368868.10(SELENBP1):​c.1045-31T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 1,593,328 control chromosomes in the GnomAD database, including 306,419 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 0.53 (22978 hom., cov: 31)
  • Exomes 𝑓: 0.62 (283441 hom.)
• Consequence: SELENBP1 ENST00000368868.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 21 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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.1045-31T>C		intron	N/A	NP_003935.2
	SELENBP1	NM_001258289.2		c.1171-31T>C		intron	N/A	NP_001245218.1
	SELENBP1	NM_001258288.2		c.859-31T>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.1045-31T>C		intron	N/A	ENSP00000357861.5
	SELENBP1	ENST00000474352.5	TSL:2	n.2197T>C		non_coding_transcript_exon	Exon 6 of 8
	SELENBP1	ENST00000426705.6	TSL:2	c.1171-31T>C		intron	N/A	ENSP00000397261.2

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80622 AN: 151848 Hom.: 22981 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.566

GnomAD2 exomes AF: 0.596 AC: 140982 AN: 236718 AF XY: 0.604

Gnomad AFR exome AF: 0.295

Gnomad AMR exome AF: 0.591

Gnomad ASJ exome AF: 0.593

Gnomad EAS exome AF: 0.595

Gnomad FIN exome AF: 0.541

Gnomad NFE exome AF: 0.636

Gnomad OTH exome AF: 0.609

GnomAD4 exome AF: 0.624 AC: 899158 AN: 1441362 Hom.: 283441 Cov.: 26 AF XY: 0.625 AC XY: 448394 AN XY: 717298

African (AFR) AF: 0.300 AC: 9899 AN: 32994

American (AMR) AF: 0.583 AC: 25162 AN: 43146

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 15340 AN: 25824

East Asian (EAS) AF: 0.541 AC: 21272 AN: 39356

South Asian (SAS) AF: 0.639 AC: 54533 AN: 85324

European-Finnish (FIN) AF: 0.545 AC: 28741 AN: 52710

Middle Eastern (MID) AF: 0.606 AC: 3250 AN: 5362

European-Non Finnish (NFE) AF: 0.642 AC: 704723 AN: 1097020

Other (OTH) AF: 0.608 AC: 36238 AN: 59626

GnomAD4 genome AF: 0.531 AC: 80645 AN: 151966 Hom.: 22978 Cov.: 31 AF XY: 0.526 AC XY: 39045 AN XY: 74252

African (AFR) AF: 0.305 AC: 12645 AN: 41418

American (AMR) AF: 0.565 AC: 8633 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2044 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2993 AN: 5158

South Asian (SAS) AF: 0.628 AC: 3032 AN: 4826

European-Finnish (FIN) AF: 0.535 AC: 5653 AN: 10562

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43586 AN: 67952

Other (OTH) AF: 0.570 AC: 1201 AN: 2108

Alfa AF: 0.607 Hom.: 15758

Bravo AF: 0.523

Asia WGS AF: 0.639 AC: 2222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.68
DANN	Benign	0.75
PhyloP100		0.10
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: rs10788804; hg19: chr1-151337788; COSMIC: COSV64373648; COSMIC: COSV64373648;