6-73241569-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030568.5(KHDC1):āc.455T>Cā(p.Ile152Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_030568.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KHDC1 | ENST00000257765.10 | c.455T>C | p.Ile152Thr | missense_variant | 4/4 | 1 | NM_030568.5 | ENSP00000257765.5 | ||
KHDC1 | ENST00000370384.7 | c.674T>C | p.Ile225Thr | missense_variant | 5/5 | 1 | ENSP00000359411.3 | |||
ENSG00000243501 | ENST00000423730.3 | n.295+486T>C | intron_variant | 5 | ENSP00000457270.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461828Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727224
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.455T>C (p.I152T) alteration is located in exon 4 (coding exon 3) of the KHDC1 gene. This alteration results from a T to C substitution at nucleotide position 455, causing the isoleucine (I) at amino acid position 152 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.