NM_032444.4:c.555C>T

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_032444.4(SLX4):c.555C>T(p.Asp185Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0604 in 1,613,964 control chromosomes in the GnomAD database, including 3,286 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.050 ( 248 hom., cov: 32)

Exomes 𝑓: 0.061 ( 3038 hom. )

Consequence

SLX4
NM_032444.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.127

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 16-3606679-G-A is Benign according to our data. Variant chr16-3606679-G-A is described in ClinVar as [Benign]. Clinvar id is 262055.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-3606679-G-A is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-0.127 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.065 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLX4	NM_032444.4 link	c.555C>T	p.Asp185Asp	synonymous_variant	Exon 3 of 15	ENST00000294008.4	NP_115820.2	Q8IY92-1
SLX4	XM_024450471.2 link	c.555C>T	p.Asp185Asp	synonymous_variant	Exon 3 of 15		XP_024306239.1
SLX4	XM_011522715.4 link	c.555C>T	p.Asp185Asp	synonymous_variant	Exon 3 of 15		XP_011521017.1
SLX4	XR_007064923.1 link	n.1204C>T		non_coding_transcript_exon_variant	Exon 3 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLX4	ENST00000294008.4 link	c.555C>T	p.Asp185Asp	synonymous_variant	Exon 3 of 15	5	NM_032444.4	ENSP00000294008.3	Q8IY92-1
SLX4	ENST00000466154.5 link	n.850C>T		non_coding_transcript_exon_variant	Exon 2 of 7	1
SLX4	ENST00000486524.1 link	n.1183C>T		non_coding_transcript_exon_variant	Exon 3 of 4	2
SLX4	ENST00000697858.1 link	n.-105C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0501

AC:

7624

AN:

152176

Hom.:

248

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0120

Gnomad AMI

AF:

0.0899

Gnomad AMR

AF:

0.0687

Gnomad ASJ

AF:

0.0187

Gnomad EAS

AF:

0.0366

Gnomad SAS

AF:

0.0528

Gnomad FIN

AF:

0.0867

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0655

Gnomad OTH

AF:

0.0492

GnomAD3 exomes

AF:

0.0583

AC:

14658

AN:

251310

Hom.:

527

AF XY:

0.0579

AC XY:

7864

AN XY:

135836

show subpopulations

Gnomad AFR exome

AF:

0.0118

Gnomad AMR exome

AF:

0.0692

Gnomad ASJ exome

AF:

0.0189

Gnomad EAS exome

AF:

0.0352

Gnomad SAS exome

AF:

0.0520

Gnomad FIN exome

AF:

0.0882

Gnomad NFE exome

AF:

0.0654

Gnomad OTH exome

AF:

0.0503

GnomAD4 exome

AF:

0.0615

AC:

89870

AN:

1461670

Hom.:

3038

Cov.:

AF XY:

0.0610

AC XY:

44334

AN XY:

727122

show subpopulations

Gnomad4 AFR exome

AF:

0.00905

Gnomad4 AMR exome

AF:

0.0654

Gnomad4 ASJ exome

AF:

0.0189

Gnomad4 EAS exome

AF:

0.0318

Gnomad4 SAS exome

AF:

0.0532

Gnomad4 FIN exome

AF:

0.0831

Gnomad4 NFE exome

AF:

0.0651

Gnomad4 OTH exome

AF:

0.0558

GnomAD4 genome

AF:

0.0500

AC:

7620

AN:

152294

Hom.:

248

Cov.:

AF XY:

0.0515

AC XY:

3833

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0120

Gnomad4 AMR

AF:

0.0684

Gnomad4 ASJ

AF:

0.0187

Gnomad4 EAS

AF:

0.0365

Gnomad4 SAS

AF:

0.0536

Gnomad4 FIN

AF:

0.0867

Gnomad4 NFE

AF:

0.0655

Gnomad4 OTH

AF:

0.0487

Alfa

AF:

0.0558

Hom.:

133

Bravo

AF:

0.0466

Asia WGS

AF:

0.0510

AC:

180

AN:

3478

EpiCase

AF:

0.0567

EpiControl

AF:

0.0584

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

- -

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. -

Aug 12, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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. -

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

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.7

DANN

Benign

0.68

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