chr20-36436110-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001365621.2(DLGAP4):c.1001T>C(p.Val334Ala) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000706 in 1,415,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 (★).
Frequency
Consequence
NM_001365621.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP4 | NM_001365621.2 | c.1001T>C | p.Val334Ala | missense_variant, splice_region_variant | 4/13 | ENST00000339266.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP4 | ENST00000339266.10 | c.1001T>C | p.Val334Ala | missense_variant, splice_region_variant | 4/13 | 5 | NM_001365621.2 | ||
DLGAP4 | ENST00000373913.7 | c.1001T>C | p.Val334Ala | missense_variant, splice_region_variant | 4/13 | 1 | |||
DLGAP4 | ENST00000373907.6 | c.1001T>C | p.Val334Ala | missense_variant, splice_region_variant | 3/12 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 7.06e-7 AC: 1AN: 1415458Hom.: 0 Cov.: 31 AF XY: 0.00000143 AC XY: 1AN XY: 701228
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2021 | The c.1001T>C (p.V334A) alteration is located in exon 3 (coding exon 2) of the DLGAP4 gene. This alteration results from a T to C substitution at nucleotide position 1001, causing the valine (V) at amino acid position 334 to be replaced by an alanine (A). 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
Publications
No publications associated with this variant yet.