15-82849724-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004839.4(HOMER2):c.1023C>T(p.Thr341=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,214 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 (★). Synonymous variant affecting the same amino acid position (i.e. T341T) has been classified as Likely benign.
Frequency
Consequence
NM_004839.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOMER2 | NM_004839.4 | c.1023C>T | p.Thr341= | synonymous_variant | 9/9 | ENST00000450735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOMER2 | ENST00000450735.7 | c.1023C>T | p.Thr341= | synonymous_variant | 9/9 | 1 | NM_004839.4 | ||
HOMER2 | ENST00000558090.2 | c.6C>T | p.Thr2= | synonymous_variant | 1/2 | 1 | |||
HOMER2 | ENST00000304231.12 | c.1056C>T | p.Thr352= | synonymous_variant | 9/9 | 5 | P1 | ||
HOMER2 | ENST00000558552.1 | n.903C>T | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000364 AC: 9AN: 247292Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134252
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460900Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726670
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 23, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at