rs140107023
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001330311.2(DVL1):āc.1366A>Gā(p.Thr456Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00321 in 1,612,314 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001330311.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DVL1 | NM_001330311.2 | c.1366A>G | p.Thr456Ala | missense_variant | 13/15 | ENST00000378888.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DVL1 | ENST00000378888.10 | c.1366A>G | p.Thr456Ala | missense_variant | 13/15 | 5 | NM_001330311.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00204 AC: 311AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00210 AC: 522AN: 248966Hom.: 0 AF XY: 0.00205 AC XY: 277AN XY: 135220
GnomAD4 exome AF: 0.00333 AC: 4860AN: 1460020Hom.: 12 Cov.: 38 AF XY: 0.00327 AC XY: 2372AN XY: 726276
GnomAD4 genome ? AF: 0.00203 AC: 309AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.00181 AC XY: 135AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:4Other:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 20, 2017 | - - |
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpretted as Likely benign and reported on 01-23-2019 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | DVL1: BP4, BS1 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2020 | - - |
DVL1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 04, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Autosomal dominant Robinow syndrome 2;C4551475:Autosomal dominant Robinow syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 16, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at