X-118975001-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001031855.3(LONRF3):c.221C>T(p.Ala74Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000461 in 1,172,340 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 21 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001031855.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LONRF3 | ENST00000371628.8 | c.221C>T | p.Ala74Val | missense_variant | Exon 1 of 11 | 1 | NM_001031855.3 | ENSP00000360690.3 | ||
LONRF3 | ENST00000304778.11 | c.221C>T | p.Ala74Val | missense_variant | Exon 1 of 10 | 1 | ENSP00000307732.7 | |||
LONRF3 | ENST00000481285.5 | n.221C>T | non_coding_transcript_exon_variant | Exon 1 of 11 | 2 | ENSP00000435426.1 |
Frequencies
GnomAD3 genomes AF: 0.0000176 AC: 2AN: 113486Hom.: 0 Cov.: 25 AF XY: 0.0000561 AC XY: 2AN XY: 35630
GnomAD3 exomes AF: 0.0000786 AC: 9AN: 114489Hom.: 0 AF XY: 0.0000538 AC XY: 2AN XY: 37143
GnomAD4 exome AF: 0.0000491 AC: 52AN: 1058854Hom.: 0 Cov.: 33 AF XY: 0.0000552 AC XY: 19AN XY: 344310
GnomAD4 genome AF: 0.0000176 AC: 2AN: 113486Hom.: 0 Cov.: 25 AF XY: 0.0000561 AC XY: 2AN XY: 35630
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.221C>T (p.A74V) alteration is located in exon 1 (coding exon 1) of the LONRF3 gene. This alteration results from a C to T substitution at nucleotide position 221, causing the alanine (A) at amino acid position 74 to be replaced by a valine (V). 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