chr6-39897271-T-C
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001201427.2(DAAM2):āc.2607T>Cā(p.Ala869=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 1,602,868 control chromosomes in the GnomAD database, including 325,204 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.68 ( 35542 hom., cov: 31)
Exomes š: 0.63 ( 289662 hom. )
Consequence
DAAM2
NM_001201427.2 synonymous
NM_001201427.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.13
Genes affected
DAAM2 (HGNC:18143): (dishevelled associated activator of morphogenesis 2) Predicted to enable actin binding activity and small GTPase binding activity. Predicted to be involved in nervous system development and regulation of Wnt signaling pathway. Predicted to act upstream of or within determination of left/right symmetry. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 6-39897271-T-C is Benign according to our data. Variant chr6-39897271-T-C is described in ClinVar as [Benign]. Clinvar id is 3059909.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.13 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAAM2 | NM_001201427.2 | c.2607T>C | p.Ala869= | synonymous_variant | 21/25 | ENST00000274867.9 | |
DAAM2-AS1 | NR_125831.1 | n.110A>G | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAAM2 | ENST00000274867.9 | c.2607T>C | p.Ala869= | synonymous_variant | 21/25 | 1 | NM_001201427.2 | P1 | |
DAAM2-AS1 | ENST00000606829.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.679 AC: 103085AN: 151898Hom.: 35495 Cov.: 31
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GnomAD3 exomes AF: 0.670 AC: 166891AN: 249060Hom.: 56977 AF XY: 0.671 AC XY: 90637AN XY: 135126
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GnomAD4 exome AF: 0.628 AC: 911276AN: 1450852Hom.: 289662 Cov.: 30 AF XY: 0.632 AC XY: 456320AN XY: 722486
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GnomAD4 genome AF: 0.679 AC: 103182AN: 152016Hom.: 35542 Cov.: 31 AF XY: 0.685 AC XY: 50876AN XY: 74292
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
DAAM2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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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