6-43017692-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_057161.4(KLHDC3):c.328G>A(p.Val110Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,610,708 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_057161.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLHDC3 | NM_057161.4 | c.328G>A | p.Val110Ile | missense_variant | 3/11 | ENST00000326974.9 | NP_476502.1 | |
KLHDC3 | XM_047418163.1 | c.328G>A | p.Val110Ile | missense_variant | 3/11 | XP_047274119.1 | ||
KLHDC3 | XM_047418164.1 | c.328G>A | p.Val110Ile | missense_variant | 3/11 | XP_047274120.1 | ||
KLHDC3 | NR_040101.2 | n.487G>A | non_coding_transcript_exon_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLHDC3 | ENST00000326974.9 | c.328G>A | p.Val110Ile | missense_variant | 3/11 | 1 | NM_057161.4 | ENSP00000313995.4 | ||
KLHDC3 | ENST00000244670.12 | c.42G>A | p.Thr14Thr | synonymous_variant | 3/10 | 1 | ENSP00000244670.8 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000113 AC: 28AN: 248122Hom.: 0 AF XY: 0.000142 AC XY: 19AN XY: 134028
GnomAD4 exome AF: 0.000118 AC: 172AN: 1458418Hom.: 0 Cov.: 31 AF XY: 0.000106 AC XY: 77AN XY: 725234
GnomAD4 genome AF: 0.000131 AC: 20AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 04, 2024 | The c.328G>A (p.V110I) alteration is located in exon 3 (coding exon 2) of the KLHDC3 gene. This alteration results from a G to A substitution at nucleotide position 328, causing the valine (V) at amino acid position 110 to be replaced by an isoleucine (I). 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