16-3581787-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_032444.4(SLX4):​c.*555C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00845 in 165,070 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0089 ( 12 hom., cov: 33)
Exomes 𝑓: 0.0028 ( 0 hom. )

Consequence

SLX4
NM_032444.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.323
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]

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 (BayesDel_noAF=-1.02).
BP6
Variant 16-3581787-G-A is Benign according to our data. Variant chr16-3581787-G-A is described in ClinVar as [Benign]. Clinvar id is 319134.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00892 (1359/152326) while in subpopulation AFR AF= 0.0244 (1016/41584). AF 95% confidence interval is 0.0232. There are 12 homozygotes in gnomad4. There are 657 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLX4NM_032444.4 linkuse as main transcriptc.*555C>T 3_prime_UTR_variant 15/15 ENST00000294008.4
SLX4XM_011522715.4 linkuse as main transcriptc.*555C>T 3_prime_UTR_variant 15/15
SLX4XM_024450471.2 linkuse as main transcriptc.*555C>T 3_prime_UTR_variant 15/15
SLX4XM_047434801.1 linkuse as main transcriptc.*555C>T 3_prime_UTR_variant 11/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLX4ENST00000294008.4 linkuse as main transcriptc.*555C>T 3_prime_UTR_variant 15/155 NM_032444.4 P1Q8IY92-1
ENST00000573982.1 linkuse as main transcriptn.198+409G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.00886
AC:
1348
AN:
152208
Hom.:
11
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0242
Gnomad AMI
AF:
0.0428
Gnomad AMR
AF:
0.00530
Gnomad ASJ
AF:
0.00375
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00785
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00216
Gnomad OTH
AF:
0.0105
GnomAD4 exome
AF:
0.00282
AC:
36
AN:
12744
Hom.:
0
Cov.:
0
AF XY:
0.00249
AC XY:
16
AN XY:
6438
show subpopulations
Gnomad4 AFR exome
AF:
0.0187
Gnomad4 AMR exome
AF:
0.00549
Gnomad4 ASJ exome
AF:
0.00296
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00246
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00194
Gnomad4 OTH exome
AF:
0.00776
GnomAD4 genome
AF:
0.00892
AC:
1359
AN:
152326
Hom.:
12
Cov.:
33
AF XY:
0.00882
AC XY:
657
AN XY:
74504
show subpopulations
Gnomad4 AFR
AF:
0.0244
Gnomad4 AMR
AF:
0.00529
Gnomad4 ASJ
AF:
0.00375
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00745
Gnomad4 FIN
AF:
0.0000941
Gnomad4 NFE
AF:
0.00216
Gnomad4 OTH
AF:
0.00993
Alfa
AF:
0.00635
Hom.:
0
Bravo
AF:
0.0101
Asia WGS
AF:
0.00231
AC:
8
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Fanconi anemia complementation group P Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This 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:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.36
DANN
Benign
0.64

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.

Other links and lift over

dbSNP: rs146163310; hg19: chr16-3631788; API