5-62579593-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_181506.5(LRRC70):c.155C>T(p.Ser52Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000774 in 1,550,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC70 | NM_181506.5 | c.155C>T | p.Ser52Leu | missense_variant | Exon 2 of 2 | ENST00000334994.6 | NP_852607.3 | |
IPO11 | NM_016338.5 | c.2583-11984C>T | intron_variant | Intron 27 of 29 | ENST00000325324.11 | NP_057422.3 | ||
IPO11 | NM_001134779.2 | c.2703-11984C>T | intron_variant | Intron 27 of 29 | NP_001128251.1 | |||
IPO11-LRRC70 | NR_073584.1 | n.201+658C>T | intron_variant | Intron 1 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC70 | ENST00000334994.6 | c.155C>T | p.Ser52Leu | missense_variant | Exon 2 of 2 | 1 | NM_181506.5 | ENSP00000399441.1 | ||
IPO11 | ENST00000325324.11 | c.2583-11984C>T | intron_variant | Intron 27 of 29 | 1 | NM_016338.5 | ENSP00000316651.6 | |||
IPO11 | ENST00000424533.5 | n.*73+110C>T | intron_variant | Intron 28 of 28 | 2 | ENSP00000395685.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000195 AC: 3AN: 153550Hom.: 0 AF XY: 0.0000368 AC XY: 3AN XY: 81462
GnomAD4 exome AF: 0.00000715 AC: 10AN: 1398888Hom.: 0 Cov.: 32 AF XY: 0.0000116 AC XY: 8AN XY: 689964
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152008Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74226
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.155C>T (p.S52L) 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 155, causing the serine (S) at amino acid position 52 to be replaced by a leucine (L). 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