NM_014846.4:c.3462G>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014846.4(WASHC5):c.3462G>T(p.Glu1154Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,610,498 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_014846.4 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WASHC5 | NM_014846.4 | c.3462G>T | p.Glu1154Asp | missense_variant | Exon 29 of 29 | ENST00000318410.12 | NP_055661.3 | |
WASHC5 | NM_001330609.2 | c.3018G>T | p.Glu1006Asp | missense_variant | Exon 28 of 28 | NP_001317538.1 | ||
WASHC5 | XM_047422502.1 | c.3462G>T | p.Glu1154Asp | missense_variant | Exon 30 of 30 | XP_047278458.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WASHC5 | ENST00000318410.12 | c.3462G>T | p.Glu1154Asp | missense_variant | Exon 29 of 29 | 1 | NM_014846.4 | ENSP00000318016.7 | ||
WASHC5 | ENST00000517845.5 | c.3018G>T | p.Glu1006Asp | missense_variant | Exon 27 of 27 | 2 | ENSP00000429676.1 | |||
WASHC5 | ENST00000519042.2 | n.601G>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251072Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135706
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1458490Hom.: 0 Cov.: 27 AF XY: 0.00000689 AC XY: 5AN XY: 725820
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152008Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74236
ClinVar
Submissions by phenotype
WASHC5-related disorder Uncertain:1
The WASHC5 c.3462G>T variant is predicted to result in the amino acid substitution p.Glu1154Asp. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at