6-45422583-A-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4BP6_ModerateBS1BS2
The ENST00000359524.7(RUNX2):c.7A>T(p.Ile3Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,505,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000359524.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUNX2 | NM_001024630.4 | c.59-10A>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000647337.2 | |||
RUNX2 | NM_001369405.1 | c.7A>T | p.Ile3Phe | missense_variant | 1/7 | ||
RUNX2 | NM_001278478.2 | c.7A>T | p.Ile3Phe | missense_variant | 1/6 | ||
RUNX2 | NM_001015051.4 | c.59-10A>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUNX2 | ENST00000647337.2 | c.59-10A>T | splice_polypyrimidine_tract_variant, intron_variant | NM_001024630.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000135 AC: 19AN: 140998Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000339 AC: 8AN: 235840Hom.: 0 AF XY: 0.0000309 AC XY: 4AN XY: 129290
GnomAD4 exome AF: 0.00000733 AC: 10AN: 1364538Hom.: 0 Cov.: 34 AF XY: 0.00000442 AC XY: 3AN XY: 678930
GnomAD4 genome ? AF: 0.000135 AC: 19AN: 141054Hom.: 0 Cov.: 29 AF XY: 0.0000885 AC XY: 6AN XY: 67798
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at