5-148120107-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PP3_ModerateBP6_Very_StrongBA1

The NM_006846.4(SPINK5):c.2412C>T(p.Gly804Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 1,612,934 control chromosomes in the GnomAD database, including 295,935 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 23520 hom., cov: 33)

Exomes 𝑓: 0.61 ( 272415 hom. )

Consequence

SPINK5
NM_006846.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.619

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 -14 ACMG points.

PP3

Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.

BP6

Variant 5-148120107-C-T is Benign according to our data. Variant chr5-148120107-C-T is described in ClinVar as [Benign]. Clinvar id is 260051.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-148120107-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPINK5	NM_006846.4 link	c.2412C>T	p.Gly804Gly	synonymous_variant	Exon 25 of 33	ENST00000256084.8	NP_006837.2	Q9NQ38-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPINK5	ENST00000256084.8 link	c.2412C>T	p.Gly804Gly	synonymous_variant	Exon 25 of 33	1	NM_006846.4	ENSP00000256084.7		Q9NQ38-1

Frequencies

GnomAD3 genomes

AF:

0.542

AC:

82396

AN:

151896

Hom.:

23497

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.595

Gnomad AMR

AF:

0.640

Gnomad ASJ

AF:

0.540

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.505

Gnomad FIN

AF:

0.633

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.629

Gnomad OTH

AF:

0.545

GnomAD3 exomes

AF:

0.594

AC:

147960

AN:

249272

Hom.:

45308

AF XY:

0.589

AC XY:

79697

AN XY:

135254

show subpopulations

Gnomad AFR exome

AF:

0.349

Gnomad AMR exome

AF:

0.742

Gnomad ASJ exome

AF:

0.550

Gnomad EAS exome

AF:

0.461

Gnomad SAS exome

AF:

0.505

Gnomad FIN exome

AF:

0.641

Gnomad NFE exome

AF:

0.622

Gnomad OTH exome

AF:

0.595

GnomAD4 exome

AF:

0.607

AC:

886052

AN:

1460920

Hom.:

272415

Cov.:

AF XY:

0.604

AC XY:

438690

AN XY:

726778

show subpopulations

Gnomad4 AFR exome

AF:

0.345

Gnomad4 AMR exome

AF:

0.726

Gnomad4 ASJ exome

AF:

0.550

Gnomad4 EAS exome

AF:

0.437

Gnomad4 SAS exome

AF:

0.509

Gnomad4 FIN exome

AF:

0.642

Gnomad4 NFE exome

AF:

0.624

Gnomad4 OTH exome

AF:

0.585

GnomAD4 genome

AF:

0.542

AC:

82459

AN:

152014

Hom.:

23520

Cov.:

AF XY:

0.542

AC XY:

40297

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.353

Gnomad4 AMR

AF:

0.641

Gnomad4 ASJ

AF:

0.540

Gnomad4 EAS

AF:

0.470

Gnomad4 SAS

AF:

0.506

Gnomad4 FIN

AF:

0.633

Gnomad4 NFE

AF:

0.629

Gnomad4 OTH

AF:

0.546

Alfa

AF:

0.593

Hom.:

16899

Bravo

AF:

0.536

Asia WGS

AF:

0.529

AC:

1833

AN:

3478

EpiCase

AF:

0.617

EpiControl

AF:

0.616

ClinVar

Significance: Benign

Submissions summary: Benign:7Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 -

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 91% of patients studied by a panel of primary immunodeficiencies. Number of patients: 80. Only high quality variants are reported. -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Netherton syndrome

Benign:2

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

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. -

Ichthyosis linearis circumflexa

Benign:1

Feb 03, 2025

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

BayesDel_noAF

Benign

-0.29

CADD

Benign

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.88

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.88

Position offset: -2

DS_DL_spliceai

0.20

Position offset: 29

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