19-4497974-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001001520.3(HDGFL2):c.1345C>T(p.Arg449Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,554,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001520.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HDGFL2 | NM_001001520.3 | c.1345C>T | p.Arg449Trp | missense_variant | Exon 11 of 16 | ENST00000616600.5 | NP_001001520.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000378 AC: 6AN: 158618Hom.: 0 AF XY: 0.0000356 AC XY: 3AN XY: 84242
GnomAD4 exome AF: 0.0000193 AC: 27AN: 1402202Hom.: 0 Cov.: 30 AF XY: 0.0000130 AC XY: 9AN XY: 691976
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1345C>T (p.R449W) alteration is located in exon 11 (coding exon 11) of the HDGFRP2 gene. This alteration results from a C to T substitution at nucleotide position 1345, causing the arginine (R) at amino acid position 449 to be replaced by a tryptophan (W). 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