NM_014159.7:c.676C>G
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_014159.7(SETD2):c.676C>G(p.Pro226Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000284 in 1,550,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014159.7 missense
Scores
Clinical Significance
Conservation
Publications
- Luscan-Lumish syndromeInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
- SETD2-related neurodevelopmental disorder without or with macrocephaly/overgrowthInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- Rabin-Pappas syndromeInheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- SETD2-related microcephaly-severe intellectual disability-multiple congenital anomalies syndromeInheritance: AD Classification: STRONG Submitted by: ClinGen
- Sotos syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- intellectual developmental disorder, autosomal dominant 70Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152232Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000126 AC: 2AN: 158504 AF XY: 0.0000120 show subpopulations
GnomAD4 exome AF: 0.0000293 AC: 41AN: 1398390Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 19AN XY: 689788 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74380 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Luscan-Lumish syndrome Benign:1Other:1
Variant interpreted as Uncertain significance and reported on 07-01-2019 by Invitae . Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Philip Payne PhD, FACMI from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at