chr8-91960320-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001198679.3(RUNX1T1):c.1914G>A(p.Pro638Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0002 in 1,611,542 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001198679.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RUNX1T1 | NM_001198679.3 | c.1914G>A | p.Pro638Pro | synonymous_variant | Exon 12 of 12 | NP_001185608.1 | ||
RUNX1T1 | NM_001395209.1 | c.1821G>A | p.Pro607Pro | synonymous_variant | Exon 12 of 12 | NP_001382138.1 | ||
RUNX1T1 | NM_001198634.2 | c.1770G>A | p.Pro590Pro | synonymous_variant | Exon 11 of 11 | NP_001185563.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152158Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000384 AC: 94AN: 244912Hom.: 1 AF XY: 0.000581 AC XY: 77AN XY: 132510
GnomAD4 exome AF: 0.000212 AC: 309AN: 1459268Hom.: 4 Cov.: 31 AF XY: 0.000328 AC XY: 238AN XY: 725712
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152274Hom.: 0 Cov.: 31 AF XY: 0.000134 AC XY: 10AN XY: 74454
ClinVar
Submissions by phenotype
RUNX1T1-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at