rs3827530

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_032444.4(SLX4):c.3662C>T(p.Ala1221Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 1,613,786 control chromosomes in the GnomAD database, including 3,256 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 0.050 ( 241 hom., cov: 32)

Exomes 𝑓: 0.061 ( 3015 hom. )

Consequence

SLX4
NM_032444.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -0.330

Variant links:

Genes affected

SLX4 (HGNC:23845): (SLX4 structure-specific endonuclease subunit) This gene encodes a protein that functions as an assembly component of multiple structure-specific endonucleases. These endonuclease complexes are required for repair of specific types of DNA lesions and critical for cellular responses to replication fork failure. Mutations in this gene were found in patients with Fanconi anemia. [provided by RefSeq, Sep 2016]

SLX4 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=0.0017294586).

BP6

Variant 16-3589976-G-A is Benign according to our data. Variant chr16-3589976-G-A is described in ClinVar as [Benign]. Clinvar id is 262048.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-3589976-G-A is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLX4	NM_032444.4 link	c.3662C>T	p.Ala1221Val	missense_variant	Exon 12 of 15	ENST00000294008.4	NP_115820.2	Q8IY92-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLX4	ENST00000294008.4 link	c.3662C>T	p.Ala1221Val	missense_variant	Exon 12 of 15	5	NM_032444.4	ENSP00000294008.3		Q8IY92-1

Frequencies

GnomAD3 genomes

AF:

0.0498

AC:

7559

AN:

151906

Hom.:

241

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.0899

Gnomad AMR

AF:

0.0689

Gnomad ASJ

AF:

0.0187

Gnomad EAS

AF:

0.0356

Gnomad SAS

AF:

0.0521

Gnomad FIN

AF:

0.0859

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0651

Gnomad OTH

AF:

0.0473

GnomAD3 exomes

AF:

0.0583

AC:

14614

AN:

250722

Hom.:

523

AF XY:

0.0579

AC XY:

7855

AN XY:

135686

show subpopulations

Gnomad AFR exome

AF:

0.0115

Gnomad AMR exome

AF:

0.0690

Gnomad ASJ exome

AF:

0.0189

Gnomad EAS exome

AF:

0.0354

Gnomad SAS exome

AF:

0.0522

Gnomad FIN exome

AF:

0.0883

Gnomad NFE exome

AF:

0.0653

Gnomad OTH exome

AF:

0.0503

GnomAD4 exome

AF:

0.0614

AC:

89737

AN:

1461762

Hom.:

3015

Cov.:

AF XY:

0.0609

AC XY:

44295

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.00920

Gnomad4 AMR exome

AF:

0.0651

Gnomad4 ASJ exome

AF:

0.0189

Gnomad4 EAS exome

AF:

0.0317

Gnomad4 SAS exome

AF:

0.0532

Gnomad4 FIN exome

AF:

0.0830

Gnomad4 NFE exome

AF:

0.0650

Gnomad4 OTH exome

AF:

0.0553

GnomAD4 genome

AF:

0.0497

AC:

7556

AN:

152024

Hom.:

241

Cov.:

AF XY:

0.0512

AC XY:

3805

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.0117

Gnomad4 AMR

AF:

0.0686

Gnomad4 ASJ

AF:

0.0187

Gnomad4 EAS

AF:

0.0355

Gnomad4 SAS

AF:

0.0530

Gnomad4 FIN

AF:

0.0859

Gnomad4 NFE

AF:

0.0651

Gnomad4 OTH

AF:

0.0468

Alfa

AF:

0.0564

Hom.:

184

Bravo

AF:

0.0464

TwinsUK

AF:

0.0612

AC:

227

ALSPAC

AF:

0.0612

AC:

236

ESP6500AA

AF:

0.0148

AC:

ESP6500EA

AF:

0.0669

AC:

575

ExAC

AF:

0.0583

AC:

7078

Asia WGS

AF:

0.0500

AC:

175

AN:

3478

EpiCase

AF:

0.0567

EpiControl

AF:

0.0583

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Fanconi anemia complementation group P

Benign:3

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 12, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 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 specified

Benign:2

Aug 31, 2012

Leiden Open Variation Database

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: curation

Curator: Arleen D. Auerbach. Submitter to LOVD: Janine Bakker. -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Feb 24, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Fanconi anemia

Benign:1

Feb 04, 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

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.2

DANN

Benign

0.93

DEOGEN2

Benign

0.016

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.42

MetaRNN

Benign

0.0017

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.34

PrimateAI

Benign

0.20

PROVEAN

Benign

-0.17

REVEL

Benign

0.0030

Sift

Benign

0.30

Sift4G

Benign

0.34

Polyphen

0.019

Vest4

0.015

MPC

0.056

ClinPred

0.00066

GERP RS

-3.8

Varity_R

0.024

gMVP

0.084

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