rs4293896
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004272.5(HOMER1):c.527+1591T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,114 control chromosomes in the GnomAD database, including 6,068 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 6068 hom., cov: 33)
Consequence
HOMER1
NM_004272.5 intron
NM_004272.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.267
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOMER1 | NM_004272.5 | c.527+1591T>G | intron_variant | ENST00000334082.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOMER1 | ENST00000334082.11 | c.527+1591T>G | intron_variant | 1 | NM_004272.5 | P1 | |||
HOMER1 | ENST00000282260.10 | c.294+13571T>G | intron_variant | 1 | |||||
HOMER1 | ENST00000508576.5 | c.527+1591T>G | intron_variant | 1 | |||||
HOMER1 | ENST00000535690.1 | c.6-35364T>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.255 AC: 38750AN: 151994Hom.: 6061 Cov.: 33
GnomAD3 genomes
?
AF:
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38750
AN:
151994
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Cov.:
33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.255 AC: 38761AN: 152114Hom.: 6068 Cov.: 33 AF XY: 0.263 AC XY: 19562AN XY: 74370
GnomAD4 genome
?
AF:
AC:
38761
AN:
152114
Hom.:
Cov.:
33
AF XY:
AC XY:
19562
AN XY:
74370
Gnomad4 AFR
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Asia WGS
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AC:
1653
AN:
3460
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at