15-82849778-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004839.4(HOMER2):c.969C>T(p.Asp323Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,613,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000054 ( 0 hom. )
Consequence
HOMER2
NM_004839.4 synonymous
NM_004839.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.988
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 15-82849778-G-A is Benign according to our data. Variant chr15-82849778-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1318090.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.988 with no splicing effect.
BS2
High AC in GnomAd4 at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HOMER2 | NM_004839.4 | c.969C>T | p.Asp323Asp | synonymous_variant | 9/9 | ENST00000450735.7 | NP_004830.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HOMER2 | ENST00000450735.7 | c.969C>T | p.Asp323Asp | synonymous_variant | 9/9 | 1 | NM_004839.4 | ENSP00000407634.2 | ||
HOMER2 | ENST00000304231.12 | c.1002C>T | p.Asp334Asp | synonymous_variant | 9/9 | 5 | ENSP00000305632.8 | |||
HOMER2 | ENST00000558552.1 | n.849C>T | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152138Hom.: 0 Cov.: 33
GnomAD3 genomes
AF:
AC:
6
AN:
152138
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000522 AC: 13AN: 249196Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135194
GnomAD3 exomes
AF:
AC:
13
AN:
249196
Hom.:
AF XY:
AC XY:
6
AN XY:
135194
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000540 AC: 79AN: 1461688Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 727124
GnomAD4 exome
AF:
AC:
79
AN:
1461688
Hom.:
Cov.:
31
AF XY:
AC XY:
45
AN XY:
727124
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74314
GnomAD4 genome
AF:
AC:
6
AN:
152138
Hom.:
Cov.:
33
AF XY:
AC XY:
4
AN XY:
74314
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 30, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at