11-644562-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_021008.4(DEAF1):c.1686G>A(p.Lys562=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,460,594 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 (★).
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.1686G>A | p.Lys562= | synonymous_variant | 12/12 | ENST00000382409.4 | |
DEAF1 | NM_001293634.1 | c.1461G>A | p.Lys487= | synonymous_variant | 11/11 | ||
DEAF1 | NM_001367390.1 | c.960G>A | p.Lys320= | synonymous_variant | 12/12 | ||
DEAF1 | XM_047426251.1 | c.960G>A | p.Lys320= | synonymous_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEAF1 | ENST00000382409.4 | c.1686G>A | p.Lys562= | synonymous_variant | 12/12 | 1 | NM_021008.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1460594Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726624
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 24, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.