rs2303063

Positions:

chr5-148100464-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006846.4(SPINK5):c.1103G>A(p.Ser368Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 1,595,430 control chromosomes in the GnomAD database, including 212,859 homozygotes. 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 Benign (★★).

Frequency

Genomes: 𝑓 0.45 ( 16486 hom., cov: 32)

Exomes 𝑓: 0.51 ( 196373 hom. )

Consequence

SPINK5
NM_006846.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7O:1

Conservation

PhyloP100: -0.0190

Variant links:

Genes affected

SPINK5 (HGNC:15464): (serine peptidase inhibitor Kazal type 5) This gene encodes a multidomain serine protease inhibitor that contains 15 potential inhibitory domains. The encoded preproprotein is proteolytically processed to generate multiple protein products, which may exhibit unique activities and specificities. These proteins may play a role in skin and hair morphogenesis, as well as anti-inflammatory and antimicrobial protection of mucous epithelia. Mutations in this gene may result in Netherton syndrome, a disorder characterized by ichthyosis, defective cornification, and atopy. This gene is present in a gene cluster on chromosome 5. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]

SPINK5 links:

FBXO38-DT (HGNC:55589): (FBXO38 divergent transcript)

FBXO38-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.628441E-6).

BP6

Variant 5-148100464-G-A is Benign according to our data. Variant chr5-148100464-G-A is described in ClinVar as [Benign]. Clinvar id is 260043.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-148100464-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPINK5	NM_006846.4 linkuse as main transcript	c.1103G>A	p.Ser368Asn	missense_variant	13/33	ENST00000256084.8	NP_006837.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPINK5	ENST00000256084.8 linkuse as main transcript	c.1103G>A	p.Ser368Asn	missense_variant	13/33	1	NM_006846.4	ENSP00000256084	P2	Q9NQ38-1
FBXO38-DT	ENST00000667608.1 linkuse as main transcript	n.1257-6722C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.447

AC:

67838

AN:

151714

Hom.:

16476

Cov.:

show subpopulations

Gnomad AFR

AF:

0.238

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.581

Gnomad ASJ

AF:

0.454

Gnomad EAS

AF:

0.475

Gnomad SAS

AF:

0.491

Gnomad FIN

AF:

0.534

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.524

Gnomad OTH

AF:

0.474

GnomAD3 exomes

AF:

0.520

AC:

129366

AN:

248890

Hom.:

35084

AF XY:

0.518

AC XY:

69924

AN XY:

135018

show subpopulations

Gnomad AFR exome

AF:

0.238

Gnomad AMR exome

AF:

0.700

Gnomad ASJ exome

AF:

0.462

Gnomad EAS exome

AF:

0.474

Gnomad SAS exome

AF:

0.487

Gnomad FIN exome

AF:

0.547

Gnomad NFE exome

AF:

0.519

Gnomad OTH exome

AF:

0.523

GnomAD4 exome

AF:

0.514

AC:

742660

AN:

1443598

Hom.:

196373

Cov.:

AF XY:

0.513

AC XY:

369137

AN XY:

719046

show subpopulations

Gnomad4 AFR exome

AF:

0.227

Gnomad4 AMR exome

AF:

0.685

Gnomad4 ASJ exome

AF:

0.461

Gnomad4 EAS exome

AF:

0.446

Gnomad4 SAS exome

AF:

0.489

Gnomad4 FIN exome

AF:

0.547

Gnomad4 NFE exome

AF:

0.521

Gnomad4 OTH exome

AF:

0.501

GnomAD4 genome

AF:

0.447

AC:

67860

AN:

151832

Hom.:

16486

Cov.:

AF XY:

0.451

AC XY:

33424

AN XY:

74170

show subpopulations

Gnomad4 AFR

AF:

0.237

Gnomad4 AMR

AF:

0.581

Gnomad4 ASJ

AF:

0.454

Gnomad4 EAS

AF:

0.474

Gnomad4 SAS

AF:

0.492

Gnomad4 FIN

AF:

0.534

Gnomad4 NFE

AF:

0.524

Gnomad4 OTH

AF:

0.476

Alfa

AF:

0.506

Hom.:

40662

Bravo

AF:

0.445

TwinsUK

AF:

0.528

AC:

1959

ALSPAC

AF:

0.526

AC:

2027

ESP6500AA

AF:

0.251

AC:

960

ESP6500EA

AF:

0.511

AC:

4223

ExAC

AF:

0.506

AC:

61104

Asia WGS

AF:

0.518

AC:

1798

AN:

3478

EpiCase

AF:

0.518

EpiControl

AF:

0.530

ClinVar

Significance: Benign

Submissions summary: Benign:7Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 28, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency. Variant hypothesized to influence skin permeability barrier and allergy. Another possible risk factor, but probably not reportable. -
Benign, criteria provided, single submitter	clinical testing	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	Jan 24, 2024	This variant is classified as Benign based on local population frequency. This variant was detected in 89% of patients studied by a panel of primary immunodeficiencies. Number of patients: 78. Only high quality variants are reported. -

Netherton syndrome

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Mar 06, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1Other:1

not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	This variant is associated with the following publications: (PMID: 11544479, 25458912, 22730493, 19534795) -

Ichthyosis linearis circumflexa

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.73

CADD

Benign

9.4

DANN

Benign

0.86

DEOGEN2

Benign

0.13

.;.;.;T

Eigen

Benign

-0.95

Eigen_PC

Benign

-0.93

FATHMM_MKL

Benign

0.041

LIST_S2

Benign

0.072

T;T;T;T

MetaRNN

Benign

0.0000066

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.6

L;L;.;L

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.50

N;N;N;N

REVEL

Benign

0.022

Sift

Benign

0.83

T;T;T;T

Sift4G

Benign

0.69

T;T;T;T

Polyphen

0.0070

B;B;.;B

Vest4

0.11

MPC

0.095

ClinPred

0.0018

GERP RS

2.4

Varity_R

0.035

gMVP

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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