9-100284480-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014425.5(INVS):c.1945G>T(p.Val649Leu) 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. 15/21 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. V649M) has been classified as Likely benign.
Frequency
Consequence
NM_014425.5 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 |
---|---|---|---|---|---|---|---|
INVS | NM_014425.5 | c.1945G>T | p.Val649Leu | missense_variant | 13/17 | ENST00000262457.7 | |
INVS | NM_001318381.2 | c.1657G>T | p.Val553Leu | missense_variant | 14/18 | ||
INVS | NM_001318382.2 | c.967G>T | p.Val323Leu | missense_variant | 13/17 | ||
INVS | NR_134606.2 | n.2143G>T | non_coding_transcript_exon_variant | 13/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INVS | ENST00000262457.7 | c.1945G>T | p.Val649Leu | missense_variant | 13/17 | 1 | NM_014425.5 | A2 | |
INVS | ENST00000262456.6 | c.1945G>T | p.Val649Leu | missense_variant | 13/18 | 5 | P4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at