chr1-45011223-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1BP4_Strong
The NM_024602.6(HECTD3):c.35C>T(p.Ser12Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00245 in 1,420,010 control chromosomes in the GnomAD database, including 3 homozygotes. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECTD3 | NM_024602.6 | c.35C>T | p.Ser12Phe | missense_variant | 1/21 | ENST00000372172.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECTD3 | ENST00000372172.5 | c.35C>T | p.Ser12Phe | missense_variant | 1/21 | 5 | NM_024602.6 | P1 | |
UROD | ENST00000652165.1 | c.-998G>A | 5_prime_UTR_variant | 1/9 |
Frequencies
GnomAD3 genomes ? AF: 0.00195 AC: 297AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00203 AC: 61AN: 30032Hom.: 0 AF XY: 0.00224 AC XY: 38AN XY: 16978
GnomAD4 exome AF: 0.00251 AC: 3177AN: 1267690Hom.: 3 Cov.: 33 AF XY: 0.00255 AC XY: 1582AN XY: 619608
GnomAD4 genome ? AF: 0.00195 AC: 297AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.00196 AC XY: 146AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.35C>T (p.S12F) 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 35, causing the serine (S) at amino acid position 12 to be replaced by a phenylalanine (F). 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