1-151365214-G-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_003944.4(SELENBP1):c.1112C>G(p.Ser371Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00165 in 1,613,884 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S371P) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0019 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0016 ( 3 hom. )

Consequence

SELENBP1
NM_003944.4 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.945

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 -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0060944855).

BP6

Variant 1-151365214-G-C is Benign according to our data. Variant chr1-151365214-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3045077.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELENBP1	NM_003944.4 link	c.1112C>G	p.Ser371Cys	missense_variant	Exon 10 of 12	ENST00000368868.10	NP_003935.2	Q13228-1V9HWG1
SELENBP1	NM_001258289.2 link	c.1238C>G	p.Ser413Cys	missense_variant	Exon 10 of 12		NP_001245218.1	Q13228-4
SELENBP1	NM_001258288.2 link	c.926C>G	p.Ser309Cys	missense_variant	Exon 9 of 11		NP_001245217.1	Q13228-3
SELENBP1	XM_047433576.1 link	c.*105C>G		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.1112C>G	p.Ser371Cys	missense_variant	Exon 10 of 12	1	NM_003944.4	ENSP00000357861.5		Q13228-1

Frequencies

GnomAD3 genomes

AF:

0.00193

AC:

293

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000507

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.00517

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00198

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00203

Gnomad OTH

AF:

0.00287

GnomAD2 exomes

AF:

0.00140

AC:

350

AN:

250424

AF XY:

0.00135

show subpopulations

Gnomad AFR exome

AF:

0.000433

Gnomad AMR exome

AF:

0.000406

Gnomad ASJ exome

AF:

0.000199

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00181

Gnomad NFE exome

AF:

0.00248

Gnomad OTH exome

AF:

0.00114

GnomAD4 exome

AF:

0.00162

AC:

2370

AN:

1461592

Hom.:

Cov.:

AF XY:

0.00152

AC XY:

1104

AN XY:

727072

show subpopulations

Gnomad4 AFR exome

AF:

0.000269

AC:

AN:

33468

Gnomad4 AMR exome

AF:

0.000828

AC:

AN:

44678

Gnomad4 ASJ exome

AF:

0.0000383

AC:

AN:

26130

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

39694

Gnomad4 SAS exome

AF:

0.0000232

AC:

AN:

86168

Gnomad4 FIN exome

AF:

0.00206

AC:

110

AN:

53412

Gnomad4 NFE exome

AF:

0.00191

AC:

2122

AN:

1111886

Gnomad4 Remaining exome

AF:

0.00147

AC:

AN:

60388

Heterozygous variant carriers

121

242

363

484

605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Variant carriers

148

222

296

370

<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:

0.00192

AC:

292

AN:

152292

Hom.:

Cov.:

AF XY:

0.00171

AC XY:

127

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.000505

AC:

0.000505172

AN:

0.000505172

Gnomad4 AMR

AF:

0.00517

AC:

0.00516542

AN:

0.00516542

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.000207

AC:

0.000207211

AN:

0.000207211

Gnomad4 FIN

AF:

0.00198

AC:

0.00197852

AN:

0.00197852

Gnomad4 NFE

AF:

0.00201

AC:

0.00201423

AN:

0.00201423

Gnomad4 OTH

AF:

0.00284

AC:

0.00284091

AN:

0.00284091

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

<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:

0.00188

Hom.:

Bravo

AF:

0.00250

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.00130

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00140

AC:

ExAC

AF:

0.00140

AC:

170

EpiCase

AF:

0.00185

EpiControl

AF:

0.00243

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SELENBP1-related disorder

Benign:1

Jun 02, 2023

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.052

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.59

CADD

Benign

6.3

DANN

Benign

0.72

DEOGEN2

Benign

0.013

T;.;.

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.042

LIST_S2

Benign

0.75

T;T;T

M_CAP

Benign

0.0034

MetaRNN

Benign

0.0061

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.70

N;.;.

PrimateAI

Benign

0.32

PROVEAN

Benign

-0.59

N;N;.

REVEL

Benign

0.045

Sift

Benign

0.13

T;T;.

Sift4G

Benign

0.11

T;T;T

Polyphen

0.0

B;.;.

Vest4

0.19

MVP

0.030

MPC

0.084

ClinPred

0.0035

GERP RS

-3.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.044

gMVP

0.35

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