chr15-82849780-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_004839.4(HOMER2):c.967G>A(p.Asp323Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. D323D) has been classified as Likely benign.
Frequency
Consequence
NM_004839.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOMER2 | NM_004839.4 | c.967G>A | p.Asp323Asn | missense_variant | 9/9 | ENST00000450735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOMER2 | ENST00000450735.7 | c.967G>A | p.Asp323Asn | missense_variant | 9/9 | 1 | NM_004839.4 | ||
HOMER2 | ENST00000304231.12 | c.1000G>A | p.Asp334Asn | missense_variant | 9/9 | 5 | P1 | ||
HOMER2 | ENST00000558552.1 | n.847G>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249208Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135202
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461694Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727128
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74326
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 323 of the HOMER2 protein (p.Asp323Asn). This variant is present in population databases (rs372825300, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with HOMER2-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at