11-694816-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000382409.4(DEAF1):āc.232A>Gā(p.Met78Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000313 in 1,438,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
ENST00000382409.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DEAF1 | NM_021008.4 | c.232A>G | p.Met78Val | missense_variant | 1/12 | ENST00000382409.4 | NP_066288.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEAF1 | ENST00000382409.4 | c.232A>G | p.Met78Val | missense_variant | 1/12 | 1 | NM_021008.4 | ENSP00000371846 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000178 AC: 27AN: 151340Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000228 AC: 2AN: 87692Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 51058
GnomAD4 exome AF: 0.0000140 AC: 18AN: 1287558Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 7AN XY: 635428
GnomAD4 genome AF: 0.000178 AC: 27AN: 151340Hom.: 0 Cov.: 32 AF XY: 0.000190 AC XY: 14AN XY: 73846
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 11, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at