chr21-46418293-T-C
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7
The NM_006031.6(PCNT):c.7011T>C(p.Asp2337Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000234 in 1,582,188 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006031.6 synonymous
Scores
Clinical Significance
Conservation
Publications
- microcephalic osteodysplastic primordial dwarfism type IIInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
- Moyamoya diseaseInheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152230Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000319 AC: 8AN: 251066 AF XY: 0.00000736 show subpopulations
GnomAD4 exome AF: 0.00000979 AC: 14AN: 1429840Hom.: 0 Cov.: 26 AF XY: 0.00000701 AC XY: 5AN XY: 713366 show subpopulations
GnomAD4 genome AF: 0.000151 AC: 23AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74500 show subpopulations
ClinVar
Submissions by phenotype
Microcephalic osteodysplastic primordial dwarfism type II Uncertain:1
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PCNT-related disorder Benign:1
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). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at