14-23275799-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020834.3(HOMEZ):c.1429C>T(p.Arg477Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,610,842 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Uncertain significance (★).
Frequency
Consequence
NM_020834.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOMEZ | NM_020834.3 | c.1429C>T | p.Arg477Trp | missense_variant | 2/2 | ENST00000357460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOMEZ | ENST00000357460.7 | c.1429C>T | p.Arg477Trp | missense_variant | 2/2 | 1 | NM_020834.3 | P2 | |
HOMEZ | ENST00000561013.3 | c.1435C>T | p.Arg479Trp | missense_variant | 3/3 | 2 | A2 | ||
HOMEZ | ENST00000673724.1 | c.1096C>T | p.Arg366Trp | missense_variant | 3/3 | A2 | |||
HOMEZ | ENST00000606731.2 | c.919C>T | p.Arg307Trp | missense_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000975 AC: 24AN: 246202Hom.: 0 AF XY: 0.0000974 AC XY: 13AN XY: 133414
GnomAD4 exome AF: 0.000106 AC: 155AN: 1458582Hom.: 1 Cov.: 36 AF XY: 0.000121 AC XY: 88AN XY: 725218
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.1429C>T (p.R477W) alteration is located in exon 2 (coding exon 2) of the HOMEZ gene. This alteration results from a C to T substitution at nucleotide position 1429, causing the arginine (R) at amino acid position 477 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