6-73363619-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001017361.3(KHDC3L):āc.413T>Cā(p.Ile138Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000824 in 1,613,410 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 Likely benign (ā ).
Frequency
Consequence
NM_001017361.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KHDC3L | NM_001017361.3 | c.413T>C | p.Ile138Thr | missense_variant | 3/3 | ENST00000370367.4 | NP_001017361.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KHDC3L | ENST00000370367.4 | c.413T>C | p.Ile138Thr | missense_variant | 3/3 | 1 | NM_001017361.3 | ENSP00000359392.3 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 151960Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249562Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135364
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1461450Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 62AN XY: 727038
GnomAD4 genome AF: 0.0000724 AC: 11AN: 151960Hom.: 0 Cov.: 32 AF XY: 0.0000809 AC XY: 6AN XY: 74208
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at