rs1270988
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001270520.2(DAAM1):c.-38+28748A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,894 control chromosomes in the GnomAD database, including 13,847 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 0.43 ( 13847 hom., cov: 31)
Consequence
DAAM1
NM_001270520.2 intron
NM_001270520.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.54
Genes affected
DAAM1 (HGNC:18142): (dishevelled associated activator of morphogenesis 1) Cell motility, adhesion, cytokinesis, and other functions of the cell cortex are mediated by reorganization of the actin cytoskeleton and several formin homology (FH) proteins have been associated with these processes. The protein encoded by this gene contains two FH domains and belongs to a novel FH protein subfamily implicated in cell polarity. A key regulator of cytoskeletal architecture, the small GTPase Rho, is activated during development by Wnt/Fz signaling to control cell polarity and movement. The protein encoded by this gene is thought to function as a scaffolding protein for the Wnt-induced assembly of a disheveled (Dvl)-Rho complex. This protein also promotes the nucleation and elongation of new actin filaments and regulates cell growth through the stabilization of microtubules. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2012]
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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=-1.02).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAAM1 | NM_001270520.2 | c.-38+28748A>C | intron_variant | ENST00000360909.8 | |||
DAAM1 | XM_005267430.3 | c.-38+28748A>C | intron_variant | ||||
DAAM1 | XM_005267431.2 | c.-38+28602A>C | intron_variant | ||||
DAAM1 | XM_047431135.1 | c.-38+28602A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAAM1 | ENST00000360909.8 | c.-38+28748A>C | intron_variant | 1 | NM_001270520.2 | P1 | |||
DAAM1 | ENST00000556596.1 | n.123+28748A>C | intron_variant, non_coding_transcript_variant | 1 | |||||
DAAM1 | ENST00000556135.1 | c.-38+28748A>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.426 AC: 64616AN: 151776Hom.: 13819 Cov.: 31
GnomAD3 genomes
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64616
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.426 AC: 64698AN: 151894Hom.: 13847 Cov.: 31 AF XY: 0.428 AC XY: 31779AN XY: 74232
GnomAD4 genome
?
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31779
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1268
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at