11-45934034-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001352027.3(PHF21A):c.1980G>A(p.Thr660Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000562 in 1,612,408 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001352027.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHF21A | NM_001352027.3 | c.1980G>A | p.Thr660Thr | synonymous_variant | Exon 19 of 19 | ENST00000676320.1 | NP_001338956.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000434 AC: 108AN: 248998Hom.: 1 AF XY: 0.000557 AC XY: 75AN XY: 134640
GnomAD4 exome AF: 0.000587 AC: 857AN: 1460252Hom.: 2 Cov.: 31 AF XY: 0.000604 AC XY: 439AN XY: 726412
GnomAD4 genome AF: 0.000322 AC: 49AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74384
ClinVar
Submissions by phenotype
not provided Benign:2
PHF21A: BP4, BP7 -
- -
PHF21A-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