7-34938060-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001366673.1(DPY19L1):c.2024G>A(p.Arg675Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,613,990 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 Likely benign (★).
Frequency
Consequence
NM_001366673.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPY19L1 | NM_001366673.1 | c.2024G>A | p.Arg675Gln | missense_variant | 21/22 | ENST00000638088.2 | NP_001353602.1 | |
DPY19L1 | NM_015283.2 | c.1805G>A | p.Arg602Gln | missense_variant | 21/22 | NP_056098.1 | ||
DPY19L1 | XM_011515246.4 | c.1937G>A | p.Arg646Gln | missense_variant | 20/21 | XP_011513548.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DPY19L1 | ENST00000638088.2 | c.2024G>A | p.Arg675Gln | missense_variant | 21/22 | 5 | NM_001366673.1 | ENSP00000490722.1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000112 AC: 28AN: 249318Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135306
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461664Hom.: 0 Cov.: 30 AF XY: 0.0000495 AC XY: 36AN XY: 727152
GnomAD4 genome AF: 0.000118 AC: 18AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | This alteration is classified as likely 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at