chr1-45011241-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024602.6(HECTD3):c.17C>T(p.Pro6Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000247 in 1,214,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024602.6 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 | UniProt |
---|---|---|---|---|---|---|---|
HECTD3 | NM_024602.6 | c.17C>T | p.Pro6Leu | missense_variant | 1/21 | ENST00000372172.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECTD3 | ENST00000372172.5 | c.17C>T | p.Pro6Leu | missense_variant | 1/21 | 5 | NM_024602.6 | P1 | |
UROD | ENST00000652165.1 | c.-980G>A | 5_prime_UTR_variant | 1/9 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000247 AC: 3AN: 1214228Hom.: 0 Cov.: 33 AF XY: 0.00000340 AC XY: 2AN XY: 587616
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2022 | The c.17C>T (p.P6L) alteration is located in exon 1 (coding exon 1) of the HECTD3 gene. This alteration results from a C to T substitution at nucleotide position 17, causing the proline (P) at amino acid position 6 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