22-39821018-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152512.4(ENTHD1):āc.807A>Cā(p.Glu269Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_152512.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENTHD1 | NM_152512.4 | c.807A>C | p.Glu269Asp | missense_variant | 5/7 | ENST00000325157.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENTHD1 | ENST00000325157.7 | c.807A>C | p.Glu269Asp | missense_variant | 5/7 | 1 | NM_152512.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251144Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135728
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461768Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 727186
GnomAD4 genome AF: 0.000131 AC: 20AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.807A>C (p.E269D) alteration is located in exon 5 (coding exon 4) of the ENTHD1 gene. This alteration results from a A to C substitution at nucleotide position 807, causing the glutamic acid (E) at amino acid position 269 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at