11-644607-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_021008.4(DEAF1):c.1641C>T(p.Thr547=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,050 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T547T) has been classified as Likely benign.
Frequency
Consequence
NM_021008.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DEAF1 | NM_021008.4 | c.1641C>T | p.Thr547= | synonymous_variant | 12/12 | ENST00000382409.4 | |
DEAF1 | NM_001293634.1 | c.1416C>T | p.Thr472= | synonymous_variant | 11/11 | ||
DEAF1 | NM_001367390.1 | c.915C>T | p.Thr305= | synonymous_variant | 12/12 | ||
DEAF1 | XM_047426251.1 | c.915C>T | p.Thr305= | synonymous_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEAF1 | ENST00000382409.4 | c.1641C>T | p.Thr547= | synonymous_variant | 12/12 | 1 | NM_021008.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249534Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135276
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460756Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726686
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at