chr15-82849950-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004839.4(HOMER2):c.844-47C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00506 in 1,582,130 control chromosomes in the GnomAD database, including 216 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 120 hom., cov: 33)
Exomes 𝑓: 0.0033 ( 96 hom. )
Consequence
HOMER2
NM_004839.4 intron
NM_004839.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.390
Genes affected
HOMER2 (HGNC:17513): (homer scaffold protein 2) This gene encodes a member of the homer family of dendritic proteins. Members of this family regulate group 1 metabotrophic glutamate receptor function. The encoded protein is a postsynaptic density scaffolding protein. Alternative splicing results in multiple transcript variants. Two related pseudogenes have been identified on chromosome 14. [provided by RefSeq, Jun 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 15-82849950-G-A is Benign according to our data. Variant chr15-82849950-G-A is described in ClinVar as [Benign]. Clinvar id is 683266.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0687 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOMER2 | NM_004839.4 | c.844-47C>T | intron_variant | ENST00000450735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOMER2 | ENST00000450735.7 | c.844-47C>T | intron_variant | 1 | NM_004839.4 | ||||
HOMER2 | ENST00000304231.12 | c.877-47C>T | intron_variant | 5 | P1 | ||||
HOMER2 | ENST00000558552.1 | n.724-47C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0215 AC: 3269AN: 152172Hom.: 121 Cov.: 33
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GnomAD3 exomes AF: 0.00711 AC: 1689AN: 237626Hom.: 47 AF XY: 0.00573 AC XY: 737AN XY: 128616
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GnomAD4 exome AF: 0.00331 AC: 4730AN: 1429840Hom.: 96 Cov.: 25 AF XY: 0.00298 AC XY: 2120AN XY: 710644
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GnomAD4 genome ? AF: 0.0215 AC: 3279AN: 152290Hom.: 120 Cov.: 33 AF XY: 0.0208 AC XY: 1550AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at