chr8-26624290-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM1PP2BP4_Moderate
The NM_001197293.3(DPYSL2):c.776C>T(p.Ala259Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000062 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. A259E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001197293.3 missense
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 |
---|---|---|---|---|---|---|---|
DPYSL2 | NM_001197293.3 | c.776C>T | p.Ala259Val | missense_variant | 4/14 | ENST00000521913.7 | |
DPYSL2 | NM_001386.6 | c.461C>T | p.Ala154Val | missense_variant | 4/14 | ||
DPYSL2 | NM_001244604.2 | c.353C>T | p.Ala118Val | missense_variant | 4/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPYSL2 | ENST00000521913.7 | c.776C>T | p.Ala259Val | missense_variant | 4/14 | 1 | NM_001197293.3 | ||
DPYSL2 | ENST00000311151.9 | c.461C>T | p.Ala154Val | missense_variant | 4/14 | 1 | P1 | ||
DPYSL2 | ENST00000523027.1 | c.353C>T | p.Ala118Val | missense_variant | 4/14 | 2 | |||
DPYSL2 | ENST00000523093.5 | n.442C>T | non_coding_transcript_exon_variant | 1/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251110Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135682
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461806Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 727192
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 05, 2023 | The c.776C>T (p.A259V) alteration is located in exon 4 (coding exon 4) of the DPYSL2 gene. This alteration results from a C to T substitution at nucleotide position 776, causing the alanine (A) at amino acid position 259 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