chr14-58645248-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000335867.4(DACT1):c.635-10T>C variant causes a splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.0000286 in 1,608,320 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 0.000046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000027 ( 0 hom. )
Consequence
DACT1
ENST00000335867.4 splice_polypyrimidine_tract, intron
ENST00000335867.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.002632
2
Clinical Significance
Conservation
PhyloP100: 4.37
Genes affected
DACT1 (HGNC:17748): (dishevelled binding antagonist of beta catenin 1) The protein encoded by this gene belongs to the dapper family, characterized by the presence of PDZ-binding motif at the C-terminus. It interacts with, and positively regulates dishevelled-mediated signaling pathways during development. Depletion of this mRNA from xenopus embryos resulted in loss of notochord and head structures, and mice lacking this gene died shortly after birth from severe posterior malformations. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 14-58645248-T-C is Benign according to our data. Variant chr14-58645248-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 795075.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DACT1 | NM_001079520.2 | c.635-121T>C | intron_variant | ENST00000395153.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DACT1 | ENST00000395153.8 | c.635-121T>C | intron_variant | 5 | NM_001079520.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000320 AC: 8AN: 250390Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135370
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GnomAD4 exome AF: 0.0000268 AC: 39AN: 1456080Hom.: 0 Cov.: 29 AF XY: 0.0000331 AC XY: 24AN XY: 724704
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74372
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 10
Find out detailed SpliceAI scores and Pangolin per-transcript scores at