3-3844978-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_020873.7(LRRN1):āc.337G>Cā(p.Val113Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,976 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 (ā ).
Frequency
Consequence
NM_020873.7 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRN1 | NM_020873.7 | c.337G>C | p.Val113Leu | missense_variant | 2/2 | ENST00000319331.4 | NP_065924.3 | |
LRRN1 | NM_001324188.2 | c.337G>C | p.Val113Leu | missense_variant | 3/3 | NP_001311117.1 | ||
LRRN1 | NM_001324189.2 | c.337G>C | p.Val113Leu | missense_variant | 3/3 | NP_001311118.1 | ||
LRRN1 | XM_047448644.1 | c.337G>C | p.Val113Leu | missense_variant | 2/2 | XP_047304600.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRN1 | ENST00000319331.4 | c.337G>C | p.Val113Leu | missense_variant | 2/2 | 1 | NM_020873.7 | ENSP00000314901 | P1 | |
SUMF1 | ENST00000448413.5 | c.1192-17469C>G | intron_variant, NMD_transcript_variant | 2 | ENSP00000404384 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251070Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135692
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461834Hom.: 0 Cov.: 76 AF XY: 0.0000124 AC XY: 9AN XY: 727220
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2024 | The c.337G>C (p.V113L) alteration is located in exon 2 (coding exon 1) of the LRRN1 gene. This alteration results from a G to C substitution at nucleotide position 337, causing the valine (V) at amino acid position 113 to be replaced by a leucine (L). 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