3-3844817-A-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_020873.7(LRRN1):āc.176A>Gā(p.Asn59Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000638 in 1,614,160 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000092 ( 0 hom., cov: 33)
Exomes š: 0.000061 ( 0 hom. )
Consequence
LRRN1
NM_020873.7 missense
NM_020873.7 missense
Scores
4
6
9
Clinical Significance
Conservation
PhyloP100: 9.25
Genes affected
LRRN1 (HGNC:20980): (leucine rich repeat neuronal 1) Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
SUMF1 (HGNC:20376): (sulfatase modifying factor 1) This gene encodes an enzyme that catalyzes the hydrolysis of sulfate esters by oxidizing a cysteine residue in the substrate sulfatase to an active site 3-oxoalanine residue, which is also known as C-alpha-formylglycine. Mutations in this gene cause multiple sulfatase deficiency, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRN1 | NM_020873.7 | c.176A>G | p.Asn59Ser | missense_variant | 2/2 | ENST00000319331.4 | NP_065924.3 | |
LRRN1 | NM_001324188.2 | c.176A>G | p.Asn59Ser | missense_variant | 3/3 | NP_001311117.1 | ||
LRRN1 | NM_001324189.2 | c.176A>G | p.Asn59Ser | missense_variant | 3/3 | NP_001311118.1 | ||
LRRN1 | XM_047448644.1 | c.176A>G | p.Asn59Ser | missense_variant | 2/2 | XP_047304600.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRN1 | ENST00000319331.4 | c.176A>G | p.Asn59Ser | missense_variant | 2/2 | 1 | NM_020873.7 | ENSP00000314901 | P1 | |
SUMF1 | ENST00000448413.5 | c.1192-17308T>C | intron_variant, NMD_transcript_variant | 2 | ENSP00000404384 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152172Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000995 AC: 25AN: 251162Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135722
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GnomAD4 exome AF: 0.0000609 AC: 89AN: 1461870Hom.: 0 Cov.: 29 AF XY: 0.0000701 AC XY: 51AN XY: 727242
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GnomAD4 genome AF: 0.0000919 AC: 14AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74462
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 19, 2022 | The c.176A>G (p.N59S) alteration is located in exon 2 (coding exon 1) of the LRRN1 gene. This alteration results from a A to G substitution at nucleotide position 176, causing the asparagine (N) at amino acid position 59 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at