5-62579458-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_181506.5(LRRC70):c.20C>T(p.Ser7Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_181506.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC70 | NM_181506.5 | c.20C>T | p.Ser7Phe | missense_variant | Exon 2 of 2 | ENST00000334994.6 | NP_852607.3 | |
IPO11 | NM_016338.5 | c.2583-12119C>T | intron_variant | Intron 27 of 29 | ENST00000325324.11 | NP_057422.3 | ||
IPO11 | NM_001134779.2 | c.2703-12119C>T | intron_variant | Intron 27 of 29 | NP_001128251.1 | |||
IPO11-LRRC70 | NR_073584.1 | n.201+523C>T | intron_variant | Intron 1 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC70 | ENST00000334994.6 | c.20C>T | p.Ser7Phe | missense_variant | Exon 2 of 2 | 1 | NM_181506.5 | ENSP00000399441.1 | ||
IPO11 | ENST00000325324.11 | c.2583-12119C>T | intron_variant | Intron 27 of 29 | 1 | NM_016338.5 | ENSP00000316651.6 | |||
IPO11 | ENST00000424533.5 | n.*48C>T | non_coding_transcript_exon_variant | Exon 28 of 29 | 2 | ENSP00000395685.1 | ||||
IPO11 | ENST00000424533.5 | n.*48C>T | 3_prime_UTR_variant | Exon 28 of 29 | 2 | ENSP00000395685.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.20C>T (p.S7F) alteration is located in exon 2 (coding exon 1) of the LRRC70 gene. This alteration results from a C to T substitution at nucleotide position 20, causing the serine (S) at amino acid position 7 to be replaced by a phenylalanine (F). 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
Publications
No publications associated with this variant yet.