Genetic Variant SELENBP1:p.Ile418Leu (chr1-151364930-T-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_003944.4(SELENBP1):c.1252A>C(p.Ile418Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)

Exomes 𝑓: 0.011 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SELENBP1
NM_003944.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.523

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 made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.13112259).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELENBP1	NM_003944.4 link	c.1252A>C	p.Ile418Leu	missense_variant	Exon 11 of 12	ENST00000368868.10	NP_003935.2	Q13228-1V9HWG1
SELENBP1	NM_001258289.2 link	c.1378A>C	p.Ile460Leu	missense_variant	Exon 11 of 12		NP_001245218.1	Q13228-4
SELENBP1	NM_001258288.2 link	c.1066A>C	p.Ile356Leu	missense_variant	Exon 10 of 11		NP_001245217.1	Q13228-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELENBP1	ENST00000368868.10 link	c.1252A>C	p.Ile418Leu	missense_variant	Exon 11 of 12	1	NM_003944.4	ENSP00000357861.5		Q13228-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

151790

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000190

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0108

AC:

15027

AN:

1385432

Hom.:

Cov.:

AF XY:

0.00988

AC XY:

6835

AN XY:

691544

show subpopulations

Gnomad4 AFR exome

AF:

0.00990

Gnomad4 AMR exome

AF:

0.000539

Gnomad4 ASJ exome

AF:

0.00443

Gnomad4 EAS exome

AF:

0.00159

Gnomad4 SAS exome

AF:

0.00363

Gnomad4 FIN exome

AF:

0.000264

Gnomad4 NFE exome

AF:

0.0131

Gnomad4 OTH exome

AF:

0.00804

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000132

AC:

AN:

151904

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000190

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Mar 23, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1252A>C (p.I418L) alteration is located in exon 11 (coding exon 11) of the SELENBP1 gene. This alteration results from a A to C substitution at nucleotide position 1252, causing the isoleucine (I) at amino acid position 418 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.0079

BayesDel_noAF

Benign

-0.25

CADD

Benign

DANN

Benign

0.92

DEOGEN2

Benign

0.049

T;.;.

Eigen

Benign

-0.53

Eigen_PC

Benign

-0.42

FATHMM_MKL

Benign

0.66

LIST_S2

Uncertain

0.90

D;D;D

M_CAP

Benign

0.0044

MetaRNN

Benign

0.13

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

L;.;.

PrimateAI

Uncertain

0.51

PROVEAN

Benign

-1.0

N;N;.

REVEL

Benign

0.14

Sift

Benign

0.27

T;T;.

Sift4G

Benign

0.16

T;T;T

Polyphen

0.0

B;.;.

Vest4

0.24

MutPred

0.33

Gain of helix (P = 0.2059);.;.;

MVP

0.10

MPC

0.091

ClinPred

0.49

GERP RS

3.2

Varity_R

0.072

gMVP

0.47

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