chr14-23275717-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.1511C>T(p.Pro504Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,610,344 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_020834.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOMEZ | NM_020834.3 | c.1511C>T | p.Pro504Leu | missense_variant | 2/2 | ENST00000357460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOMEZ | ENST00000357460.7 | c.1511C>T | p.Pro504Leu | missense_variant | 2/2 | 1 | NM_020834.3 | P2 | |
HOMEZ | ENST00000561013.3 | c.1517C>T | p.Pro506Leu | missense_variant | 3/3 | 2 | A2 | ||
HOMEZ | ENST00000673724.1 | c.1178C>T | p.Pro393Leu | missense_variant | 3/3 | A2 | |||
HOMEZ | ENST00000606731.2 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152004Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000412 AC: 1AN: 242868Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131498
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458340Hom.: 0 Cov.: 35 AF XY: 0.00000276 AC XY: 2AN XY: 725132
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152004Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74238
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.1511C>T (p.P504L) 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 1511, causing the proline (P) at amino acid position 504 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