chr7-111123833-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001099658.2(LRRN3):c.1061T>C(p.Ile354Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099658.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRN3 | NM_001099658.2 | c.1061T>C | p.Ile354Thr | missense_variant | 3/3 | ENST00000308478.10 | |
IMMP2L | NM_032549.4 | c.240-160268A>G | intron_variant | ENST00000405709.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRN3 | ENST00000308478.10 | c.1061T>C | p.Ile354Thr | missense_variant | 3/3 | 1 | NM_001099658.2 | P1 | |
IMMP2L | ENST00000405709.7 | c.240-160268A>G | intron_variant | 1 | NM_032549.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250998Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135644
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461724Hom.: 0 Cov.: 34 AF XY: 0.0000385 AC XY: 28AN XY: 727156
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.1061T>C (p.I354T) alteration is located in exon 4 (coding exon 1) of the LRRN3 gene. This alteration results from a T to C substitution at nucleotide position 1061, causing the isoleucine (I) at amino acid position 354 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at