rs1135402753
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_025257.3(SLC44A4):c.466A>G(p.Met156Val) variant causes a missense, splice region 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. 15/24 in silico tools predict a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_025257.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC44A4 | NM_025257.3 | c.466A>G | p.Met156Val | missense_variant, splice_region_variant | 6/21 | ENST00000229729.11 | |
SLC44A4 | NM_001178045.2 | c.238A>G | p.Met80Val | missense_variant, splice_region_variant | 6/21 | ||
SLC44A4 | NM_001178044.2 | c.343-203A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC44A4 | ENST00000229729.11 | c.466A>G | p.Met156Val | missense_variant, splice_region_variant | 6/21 | 1 | NM_025257.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Hearing loss, autosomal dominant 72 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 19, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at