rs138447102
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_021008.4(DEAF1):c.1186G>A(p.Gly396Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00117 in 1,614,020 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_021008.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DEAF1 | NM_021008.4 | c.1186G>A | p.Gly396Ser | missense_variant | 9/12 | ENST00000382409.4 | NP_066288.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEAF1 | ENST00000382409.4 | c.1186G>A | p.Gly396Ser | missense_variant | 9/12 | 1 | NM_021008.4 | ENSP00000371846.3 |
Frequencies
GnomAD3 genomes AF: 0.000861 AC: 131AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000732 AC: 184AN: 251454Hom.: 0 AF XY: 0.000736 AC XY: 100AN XY: 135900
GnomAD4 exome AF: 0.00120 AC: 1754AN: 1461848Hom.: 1 Cov.: 31 AF XY: 0.00120 AC XY: 875AN XY: 727224
GnomAD4 genome AF: 0.000861 AC: 131AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.000794 AC XY: 59AN XY: 74320
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 11, 2017 | - - |
Intellectual disability-epilepsy-extrapyramidal syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Jun 18, 2020 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 11, 2022 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
DEAF1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 17, 2020 | 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