chr12-105107851-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015275.3(WASHC4):c.51C>G(p.Asp17Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000729 in 1,549,918 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D17N) has been classified as Likely benign.
Frequency
Consequence
NM_015275.3 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 |
---|---|---|---|---|---|---|---|
WASHC4 | NM_015275.3 | c.51C>G | p.Asp17Glu | missense_variant | 1/33 | ENST00000332180.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WASHC4 | ENST00000332180.10 | c.51C>G | p.Asp17Glu | missense_variant | 1/33 | 1 | NM_015275.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000228 AC: 35AN: 153182Hom.: 0 AF XY: 0.000197 AC XY: 16AN XY: 81236
GnomAD4 exome AF: 0.0000737 AC: 103AN: 1397768Hom.: 0 Cov.: 29 AF XY: 0.0000827 AC XY: 57AN XY: 689584
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.51C>G (p.D17E) alteration is located in exon 1 (coding exon 1) of the KIAA1033 gene. This alteration results from a C to G substitution at nucleotide position 51, causing the aspartic acid (D) at amino acid position 17 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at