1-151365227-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_003944.4(SELENBP1):c.1099G>A(p.Glu367Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,613,590 control chromosomes in the GnomAD database, including 143 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 14 hom., cov: 32)

Exomes 𝑓: 0.011 ( 129 hom. )

Consequence

SELENBP1
NM_003944.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.25

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0027176738).

BP6

Variant 1-151365227-C-T is Benign according to our data. Variant chr1-151365227-C-T is described in ClinVar as [Benign]. Clinvar id is 775140.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-151365227-C-T is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population mid. GnomAdExome4 allele frequency = 0.0114 (16709/1461342) while in subpopulation MID AF = 0.0193 (111/5764). AF 95% confidence interval is 0.0164. There are 129 homozygotes in GnomAdExome4. There are 8146 alleles in the male GnomAdExome4 subpopulation. Median coverage is 31. This position FAILED quality control check.

BS2

High Homozygotes in GnomAd4 at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELENBP1	NM_003944.4 link	c.1099G>A	p.Glu367Lys	missense_variant	Exon 10 of 12	ENST00000368868.10	NP_003935.2	Q13228-1V9HWG1
SELENBP1	NM_001258289.2 link	c.1225G>A	p.Glu409Lys	missense_variant	Exon 10 of 12		NP_001245218.1	Q13228-4
SELENBP1	NM_001258288.2 link	c.913G>A	p.Glu305Lys	missense_variant	Exon 9 of 11		NP_001245217.1	Q13228-3
SELENBP1	XM_047433576.1 link	c.*92G>A		3_prime_UTR_variant	Exon 9 of 9		XP_047289532.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELENBP1	ENST00000368868.10 link	c.1099G>A	p.Glu367Lys	missense_variant	Exon 10 of 12	1	NM_003944.4	ENSP00000357861.5		Q13228-1

Frequencies

GnomAD3 genomes

AF:

0.0116

AC:

1760

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0156

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0110

Gnomad ASJ

AF:

0.0135

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00704

Gnomad FIN

AF:

0.000659

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0120

Gnomad OTH

AF:

0.0134

GnomAD2 exomes

AF:

0.00930

AC:

2323

AN:

249836

AF XY:

0.00890

show subpopulations

Gnomad AFR exome

AF:

0.0171

Gnomad AMR exome

AF:

0.00874

Gnomad ASJ exome

AF:

0.0133

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000931

Gnomad NFE exome

AF:

0.0119

Gnomad OTH exome

AF:

0.0110

GnomAD4 exome

AF:

0.0114

AC:

16709

AN:

1461342

Hom.:

129

Cov.:

AF XY:

0.0112

AC XY:

8146

AN XY:

726956

show subpopulations

Gnomad4 AFR exome

AF:

0.0157

AC:

526

AN:

33464

Gnomad4 AMR exome

AF:

0.00893

AC:

399

AN:

44662

Gnomad4 ASJ exome

AF:

0.0133

AC:

347

AN:

26126

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

39680

Gnomad4 SAS exome

AF:

0.00639

AC:

550

AN:

86138

Gnomad4 FIN exome

AF:

0.00116

AC:

AN:

53392

Gnomad4 NFE exome

AF:

0.0126

AC:

13976

AN:

1111742

Gnomad4 Remaining exome

AF:

0.0122

AC:

738

AN:

60374

Heterozygous variant carriers

841

1683

2524

3366

4207

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

540

1080

1620

2160

2700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0116

AC:

1761

AN:

152248

Hom.:

Cov.:

AF XY:

0.00997

AC XY:

742

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.0156

AC:

0.0156476

AN:

0.0156476

Gnomad4 AMR

AF:

0.0110

AC:

0.0109861

AN:

0.0109861

Gnomad4 ASJ

AF:

0.0135

AC:

0.0135447

AN:

0.0135447

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.00725

AC:

0.00725238

AN:

0.00725238

Gnomad4 FIN

AF:

0.000659

AC:

0.000659258

AN:

0.000659258

Gnomad4 NFE

AF:

0.0120

AC:

0.0120291

AN:

0.0120291

Gnomad4 OTH

AF:

0.0132

AC:

0.013245

AN:

0.013245

Heterozygous variant carriers

196

294

392

490

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0116

Hom.:

Bravo

AF:

0.0128

TwinsUK

AF:

0.0135

AC:

ALSPAC

AF:

0.0166

AC:

ESP6500AA

AF:

0.0148

AC:

ESP6500EA

AF:

0.0121

AC:

104

ExAC

AF:

0.00915

AC:

1111

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.0137

EpiControl

AF:

0.0137

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 27, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.82

DEOGEN2

Benign

0.014

T;.;.

Eigen

Benign

-0.87

Eigen_PC

Benign

-0.70

FATHMM_MKL

Benign

0.61

LIST_S2

Benign

0.66

T;T;T

MetaRNN

Benign

0.0027

T;T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-0.035

N;.;.

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.47

N;N;.

REVEL

Benign

0.046

Sift

Benign

0.67

T;T;.

Sift4G

Benign

0.73

T;T;T

Polyphen

0.0

B;.;.

Vest4

0.16

MVP

0.076

MPC

0.098

ClinPred

0.0074

GERP RS

1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.023

gMVP

0.37

Mutation Taster

=100/0

polymorphism

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over