5-179820902-G-C

Variant summary

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

The NM_001142298.2(SQSTM1):​c.-47-2056G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00332 in 1,473,186 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.014 ( 45 hom., cov: 34)
Exomes 𝑓: 0.0021 ( 35 hom. )

Consequence

SQSTM1
NM_001142298.2 intron

Scores

2

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.98
Variant links:
Genes affected
SQSTM1 (HGNC:11280): (sequestosome 1) This gene encodes a multifunctional protein that binds ubiquitin and regulates activation of the nuclear factor kappa-B (NF-kB) signaling pathway. The protein functions as a scaffolding/adaptor protein in concert with TNF receptor-associated factor 6 to mediate activation of NF-kB in response to upstream signals. Alternatively spliced transcript variants encoding either the same or different isoforms have been identified for this gene. Mutations in this gene result in sporadic and familial Paget disease of bone. [provided by RefSeq, Mar 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 5-179820902-G-C is Benign according to our data. Variant chr5-179820902-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 353151.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 = 0.0138 (2094/152286) while in subpopulation AFR AF= 0.0438 (1819/41574). AF 95% confidence interval is 0.0421. There are 45 homozygotes in gnomad4. There are 1007 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2094 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SQSTM1NM_001142298.2 linkc.-47-2056G>C intron_variant Intron 2 of 8 NP_001135770.1 Q13501-2
SQSTM1NM_001142299.2 linkc.-47-2056G>C intron_variant Intron 2 of 8 NP_001135771.1 Q13501-2
SQSTM1NM_003900.5 linkc.-35G>C upstream_gene_variant ENST00000389805.9 NP_003891.1 Q13501-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SQSTM1ENST00000389805.9 linkc.-35G>C upstream_gene_variant 1 NM_003900.5 ENSP00000374455.4 Q13501-1

Frequencies

GnomAD3 genomes
AF:
0.0137
AC:
2085
AN:
152178
Hom.:
45
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0437
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0118
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.000970
Gnomad OTH
AF:
0.0129
GnomAD3 exomes
AF:
0.00276
AC:
327
AN:
118572
Hom.:
5
AF XY:
0.00245
AC XY:
168
AN XY:
68496
show subpopulations
Gnomad AFR exome
AF:
0.0450
Gnomad AMR exome
AF:
0.00409
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000261
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000975
Gnomad OTH exome
AF:
0.00264
GnomAD4 exome
AF:
0.00212
AC:
2797
AN:
1320900
Hom.:
35
Cov.:
30
AF XY:
0.00199
AC XY:
1286
AN XY:
647604
show subpopulations
Gnomad4 AFR exome
AF:
0.0462
Gnomad4 AMR exome
AF:
0.00501
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000332
Gnomad4 SAS exome
AF:
0.000243
Gnomad4 FIN exome
AF:
0.000112
Gnomad4 NFE exome
AF:
0.00104
Gnomad4 OTH exome
AF:
0.00451
GnomAD4 genome
AF:
0.0138
AC:
2094
AN:
152286
Hom.:
45
Cov.:
34
AF XY:
0.0135
AC XY:
1007
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.0438
Gnomad4 AMR
AF:
0.0118
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000971
Gnomad4 OTH
AF:
0.0128
Alfa
AF:
0.00229
Hom.:
2
Bravo
AF:
0.0156

ClinVar

Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Jul 03, 2018
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Bone Paget disease Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely 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
-0.81
CADD
Benign
2.6
DANN
Benign
0.39

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: rs189132632; hg19: chr5-179247902; API