chr6-73224169-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001126063.3(KHDC1L):āc.292C>Gā(p.Arg98Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000256 in 1,406,480 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_001126063.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KHDC1L | NM_001126063.3 | c.292C>G | p.Arg98Gly | missense_variant | 2/3 | ENST00000370388.4 | NP_001119535.1 | |
LOC122539213 | NR_173145.1 | n.1471C>G | non_coding_transcript_exon_variant | 7/8 | ||||
LOC122539213 | NR_173146.1 | n.1264C>G | non_coding_transcript_exon_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KHDC1L | ENST00000370388.4 | c.292C>G | p.Arg98Gly | missense_variant | 2/3 | 1 | NM_001126063.3 | ENSP00000359415.3 | ||
ENSG00000243501 | ENST00000423730.3 | n.*84C>G | non_coding_transcript_exon_variant | 5/8 | 5 | ENSP00000457270.2 | ||||
ENSG00000243501 | ENST00000423730.3 | n.*84C>G | 3_prime_UTR_variant | 5/8 | 5 | ENSP00000457270.2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.0000256 AC: 36AN: 1406480Hom.: 0 Cov.: 31 AF XY: 0.0000259 AC XY: 18AN XY: 694534
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.292C>G (p.R98G) alteration is located in exon 2 (coding exon 2) of the KHDC1L gene. This alteration results from a C to G substitution at nucleotide position 292, causing the arginine (R) at amino acid position 98 to be replaced by a glycine (G). 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