chr1-110951455-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_018372.4(LRIF1):c.1429A>G(p.Ile477Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018372.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRIF1 | NM_018372.4 | c.1429A>G | p.Ile477Val | missense_variant | 2/4 | ENST00000369763.5 | |
LRIF1 | XM_005271029.5 | c.1429A>G | p.Ile477Val | missense_variant | 2/4 | ||
LRIF1 | XM_017001769.3 | c.1429A>G | p.Ile477Val | missense_variant | 2/4 | ||
LRIF1 | NM_001006945.2 | c.-12-1332A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIF1 | ENST00000369763.5 | c.1429A>G | p.Ile477Val | missense_variant | 2/4 | 5 | NM_018372.4 | P1 | |
ENST00000440689.1 | n.1695-729T>C | intron_variant, non_coding_transcript_variant | 2 | ||||||
LRIF1 | ENST00000485275.2 | c.-12-1332A>G | intron_variant | 2 | |||||
LRIF1 | ENST00000494675.5 | c.-13+1077A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251354Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135842
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461844Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727222
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74332
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at