chr6-73241560-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030568.5(KHDC1):c.464C>T(p.Ser155Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000188 in 1,613,956 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 (★).
Frequency
Consequence
NM_030568.5 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 |
---|---|---|---|---|---|---|---|
KHDC1 | NM_030568.5 | c.464C>T | p.Ser155Leu | missense_variant | 4/4 | ENST00000257765.10 | |
LOC122539213 | NR_173146.1 | n.959+495C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KHDC1 | ENST00000257765.10 | c.464C>T | p.Ser155Leu | missense_variant | 4/4 | 1 | NM_030568.5 | P2 | |
KHDC1 | ENST00000370384.7 | c.683C>T | p.Ser228Leu | missense_variant | 5/5 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152056Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000761 AC: 19AN: 249516Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135376
GnomAD4 exome AF: 0.000188 AC: 275AN: 1461782Hom.: 0 Cov.: 31 AF XY: 0.000186 AC XY: 135AN XY: 727184
GnomAD4 genome AF: 0.000184 AC: 28AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | The c.464C>T (p.S155L) alteration is located in exon 4 (coding exon 3) of the KHDC1 gene. This alteration results from a C to T substitution at nucleotide position 464, causing the serine (S) at amino acid position 155 to be replaced by a leucine (L). 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