chr19-4670219-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019107.4(MYDGF):c.116C>A(p.Ala39Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000016 in 1,563,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A39S) has been classified as Uncertain significance.
Frequency
Consequence
NM_019107.4 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 |
---|---|---|---|---|---|---|---|
MYDGF | NM_019107.4 | c.116C>A | p.Ala39Glu | missense_variant | 1/6 | ENST00000262947.8 | |
MYDGF | XM_017026987.2 | c.116C>A | p.Ala39Glu | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYDGF | ENST00000262947.8 | c.116C>A | p.Ala39Glu | missense_variant | 1/6 | 1 | NM_019107.4 | P1 | |
MYDGF | ENST00000599630.1 | c.116C>A | p.Ala39Glu | missense_variant | 1/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 3AN: 188620Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 106224
GnomAD4 exome AF: 0.00000709 AC: 10AN: 1410898Hom.: 0 Cov.: 33 AF XY: 0.00000999 AC XY: 7AN XY: 701034
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152332Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.116C>A (p.A39E) alteration is located in exon 1 (coding exon 1) of the MYDGF gene. This alteration results from a C to A substitution at nucleotide position 116, causing the alanine (A) at amino acid position 39 to be replaced by a glutamic acid (E). 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