6-45422681-ACAGCAGCAGCAACAGCAGCAGCAGCAACAG-A
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001024630.4(RUNX2):c.159_188delACAGCAGCAGCAGCAACAGCAGCAGCAGCA(p.Gln54_Gln63del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,450,906 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q53Q) has been classified as Likely benign.
Frequency
Consequence
NM_001024630.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
Publications
- cleidocranial dysplasia 1Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, G2P, Labcorp Genetics (formerly Invitae)
- metaphyseal dysplasia-maxillary hypoplasia-brachydacty syndromeInheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RUNX2 | NM_001024630.4 | c.159_188delACAGCAGCAGCAGCAACAGCAGCAGCAGCA | p.Gln54_Gln63del | disruptive_inframe_deletion | Exon 3 of 9 | ENST00000647337.2 | NP_001019801.3 | |
RUNX2 | NM_001369405.1 | c.117_146delACAGCAGCAGCAGCAACAGCAGCAGCAGCA | p.Gln40_Gln49del | disruptive_inframe_deletion | Exon 1 of 7 | NP_001356334.1 | ||
RUNX2 | NM_001015051.4 | c.159_188delACAGCAGCAGCAGCAACAGCAGCAGCAGCA | p.Gln54_Gln63del | disruptive_inframe_deletion | Exon 3 of 8 | NP_001015051.3 | ||
RUNX2 | NM_001278478.2 | c.117_146delACAGCAGCAGCAGCAACAGCAGCAGCAGCA | p.Gln40_Gln49del | disruptive_inframe_deletion | Exon 1 of 6 | NP_001265407.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1450906Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 721666 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at