6-73242170-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030568.5(KHDC1):c.180G>T(p.Trp60Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,614,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.180G>T | p.Trp60Cys | missense_variant | 3/4 | 1 | NM_030568.5 | ENSP00000257765.5 | ||
KHDC1 | ENST00000370384.7 | c.399G>T | p.Trp133Cys | missense_variant | 4/5 | 1 | ENSP00000359411.3 | |||
ENSG00000243501 | ENST00000423730.3 | n.180G>T | non_coding_transcript_exon_variant | 3/8 | 5 | ENSP00000457270.2 | ||||
KHDC1 | ENST00000433730.1 | c.180G>T | p.Trp60Cys | missense_variant | 3/3 | 3 | ENSP00000406966.1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000642 AC: 16AN: 249294Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135254
GnomAD4 exome AF: 0.0000636 AC: 93AN: 1461866Hom.: 0 Cov.: 32 AF XY: 0.0000550 AC XY: 40AN XY: 727230
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.180G>T (p.W60C) alteration is located in exon 3 (coding exon 2) of the KHDC1 gene. This alteration results from a G to T substitution at nucleotide position 180, causing the tryptophan (W) at amino acid position 60 to be replaced by a cysteine (C). 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