3-3845471-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_020873.7(LRRN1):āc.830A>Gā(p.Lys277Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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 | UniProt |
---|---|---|---|---|---|---|---|
LRRN1 | NM_020873.7 | c.830A>G | p.Lys277Arg | missense_variant | 2/2 | ENST00000319331.4 | |
LRRN1 | NM_001324188.2 | c.830A>G | p.Lys277Arg | missense_variant | 3/3 | ||
LRRN1 | NM_001324189.2 | c.830A>G | p.Lys277Arg | missense_variant | 3/3 | ||
LRRN1 | XM_047448644.1 | c.830A>G | p.Lys277Arg | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRN1 | ENST00000319331.4 | c.830A>G | p.Lys277Arg | missense_variant | 2/2 | 1 | NM_020873.7 | P1 | |
SUMF1 | ENST00000448413.5 | c.1192-17962T>C | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250294Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135646
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461882Hom.: 0 Cov.: 75 AF XY: 0.0000110 AC XY: 8AN XY: 727244
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2023 | The c.830A>G (p.K277R) 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 830, causing the lysine (K) at amino acid position 277 to be replaced by an arginine (R). 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