chr7-34969525-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001366673.1(DPY19L1):c.922A>C(p.Lys308Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000388 in 1,548,322 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001366673.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPY19L1 | NM_001366673.1 | c.922A>C | p.Lys308Gln | missense_variant | 9/22 | ENST00000638088.2 | |
DPY19L1 | NM_015283.2 | c.703A>C | p.Lys235Gln | missense_variant | 9/22 | ||
DPY19L1 | XM_011515246.4 | c.922A>C | p.Lys308Gln | missense_variant | 9/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPY19L1 | ENST00000638088.2 | c.922A>C | p.Lys308Gln | missense_variant | 9/22 | 5 | NM_001366673.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000494 AC: 1AN: 202420Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 110704
GnomAD4 exome AF: 7.16e-7 AC: 1AN: 1395986Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 693628
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.703A>C (p.K235Q) alteration is located in exon 9 (coding exon 9) of the DPY19L1 gene. This alteration results from a A to C substitution at nucleotide position 703, causing the lysine (K) at amino acid position 235 to be replaced by a glutamine (Q). 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