1-110951337-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018372.4(LRIF1):c.1547C>G(p.Ala516Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000805 in 1,613,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A516E) has been classified as Uncertain significance.
Frequency
Consequence
NM_018372.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRIF1 | NM_018372.4 | c.1547C>G | p.Ala516Gly | missense_variant | 2/4 | ENST00000369763.5 | |
LRIF1 | XM_005271029.5 | c.1547C>G | p.Ala516Gly | missense_variant | 2/4 | ||
LRIF1 | XM_017001769.3 | c.1547C>G | p.Ala516Gly | missense_variant | 2/4 | ||
LRIF1 | NM_001006945.2 | c.-12-1214C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIF1 | ENST00000369763.5 | c.1547C>G | p.Ala516Gly | missense_variant | 2/4 | 5 | NM_018372.4 | P1 | |
ENST00000440689.1 | n.1695-847G>C | intron_variant, non_coding_transcript_variant | 2 | ||||||
LRIF1 | ENST00000485275.2 | c.-12-1214C>G | intron_variant | 2 | |||||
LRIF1 | ENST00000494675.5 | c.-13+1195C>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251200Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135772
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461772Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727190
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2024 | The c.1547C>G (p.A516G) alteration is located in exon 2 (coding exon 2) of the LRIF1 gene. This alteration results from a C to G substitution at nucleotide position 1547, causing the alanine (A) at amino acid position 516 to be replaced by a glycine (G). 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