1-36394018-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032881.3(LSM10):c.112G>A(p.Val38Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,614,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_032881.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LSM10 | ENST00000315732.3 | c.112G>A | p.Val38Met | missense_variant | Exon 2 of 2 | 1 | NM_032881.3 | ENSP00000319341.2 | ||
LSM10 | ENST00000476041.1 | n.257G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 | |||||
LSM10 | ENST00000489912.1 | n.397G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251472Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135918
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727248
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152350Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74500
ClinVar
Submissions by phenotype
Fraser syndrome 3 Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at