chr7-34966896-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001366673.1(DPY19L1):c.1090A>G(p.Met364Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000157 in 1,525,566 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. 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. M364L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001366673.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPY19L1 | NM_001366673.1 | c.1090A>G | p.Met364Val | missense_variant, splice_region_variant | 10/22 | ENST00000638088.2 | |
DPY19L1 | NM_015283.2 | c.871A>G | p.Met291Val | missense_variant, splice_region_variant | 10/22 | ||
DPY19L1 | XM_011515246.4 | c.1090A>G | p.Met364Val | missense_variant, splice_region_variant | 10/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPY19L1 | ENST00000638088.2 | c.1090A>G | p.Met364Val | missense_variant, splice_region_variant | 10/22 | 5 | NM_001366673.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000310 AC: 6AN: 193766Hom.: 0 AF XY: 0.00000940 AC XY: 1AN XY: 106408
GnomAD4 exome AF: 0.0000146 AC: 20AN: 1373402Hom.: 0 Cov.: 28 AF XY: 0.00000879 AC XY: 6AN XY: 682976
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 12, 2023 | The c.871A>G (p.M291V) alteration is located in exon 10 (coding exon 10) of the DPY19L1 gene. This alteration results from a A to G substitution at nucleotide position 871, causing the methionine (M) at amino acid position 291 to be replaced by a valine (V). 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