2-100299849-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198461.4(LONRF2):c.1135C>T(p.His379Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000822 in 1,460,308 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198461.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LONRF2 | NM_198461.4 | c.1135C>T | p.His379Tyr | missense_variant | 5/12 | ENST00000393437.8 | NP_940863.3 | |
LONRF2 | NM_001371783.1 | c.406C>T | p.His136Tyr | missense_variant | 6/13 | NP_001358712.1 | ||
LONRF2 | XM_047443537.1 | c.406C>T | p.His136Tyr | missense_variant | 5/12 | XP_047299493.1 | ||
LONRF2 | XM_047443538.1 | c.1135C>T | p.His379Tyr | missense_variant | 5/6 | XP_047299494.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LONRF2 | ENST00000393437.8 | c.1135C>T | p.His379Tyr | missense_variant | 5/12 | 5 | NM_198461.4 | ENSP00000377086.3 | ||
LONRF2 | ENST00000409647.1 | c.406C>T | p.His136Tyr | missense_variant | 5/12 | 2 | ENSP00000386823.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251186Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135764
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460308Hom.: 0 Cov.: 33 AF XY: 0.00000826 AC XY: 6AN XY: 726602
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 10, 2023 | The c.1135C>T (p.H379Y) alteration is located in exon 5 (coding exon 5) of the LONRF2 gene. This alteration results from a C to T substitution at nucleotide position 1135, causing the histidine (H) at amino acid position 379 to be replaced by a tyrosine (Y). 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