1-110951520-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018372.4(LRIF1):c.1364C>A(p.Thr455Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000688 in 1,614,020 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 Uncertain significance (★).
Frequency
Consequence
NM_018372.4 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 | UniProt |
---|---|---|---|---|---|---|---|
LRIF1 | NM_018372.4 | c.1364C>A | p.Thr455Lys | missense_variant | 2/4 | ENST00000369763.5 | |
LRIF1 | XM_005271029.5 | c.1364C>A | p.Thr455Lys | missense_variant | 2/4 | ||
LRIF1 | XM_017001769.3 | c.1364C>A | p.Thr455Lys | missense_variant | 2/4 | ||
LRIF1 | NM_001006945.2 | c.-12-1397C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIF1 | ENST00000369763.5 | c.1364C>A | p.Thr455Lys | missense_variant | 2/4 | 5 | NM_018372.4 | P1 | |
ENST00000440689.1 | n.1695-664G>T | intron_variant, non_coding_transcript_variant | 2 | ||||||
LRIF1 | ENST00000485275.2 | c.-12-1397C>A | intron_variant | 2 | |||||
LRIF1 | ENST00000494675.5 | c.-13+1012C>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251094Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135682
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461830Hom.: 0 Cov.: 31 AF XY: 0.0000798 AC XY: 58AN XY: 727214
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.1364C>A (p.T455K) alteration is located in exon 2 (coding exon 2) of the LRIF1 gene. This alteration results from a C to A substitution at nucleotide position 1364, causing the threonine (T) at amino acid position 455 to be replaced by a lysine (K). 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