NM_032881.3:c.262G>C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032881.3(LSM10):āc.262G>Cā(p.Val88Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V88M) has been classified as Uncertain significance.
Frequency
Consequence
NM_032881.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LSM10 | ENST00000315732.3 | c.262G>C | p.Val88Leu | missense_variant | Exon 2 of 2 | 1 | NM_032881.3 | ENSP00000319341.2 | ||
LSM10 | ENST00000476041.1 | n.407G>C | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 | |||||
LSM10 | ENST00000489912.1 | n.*146G>C | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251478Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135922
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727248
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74518
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at