chr1-34905251-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001080418.3(DLGAP3):c.133C>A(p.Pro45Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000116 in 1,592,980 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P45H) has been classified as Likely benign.
Frequency
Consequence
NM_001080418.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP3 | NM_001080418.3 | c.133C>A | p.Pro45Thr | missense_variant | 3/12 | ENST00000373347.6 | |
DLGAP3 | XM_011541879.3 | c.133C>A | p.Pro45Thr | missense_variant | 4/13 | ||
DLGAP3 | XM_047426631.1 | c.133C>A | p.Pro45Thr | missense_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP3 | ENST00000373347.6 | c.133C>A | p.Pro45Thr | missense_variant | 3/12 | 5 | NM_001080418.3 | P1 | |
DLGAP3 | ENST00000235180.4 | c.133C>A | p.Pro45Thr | missense_variant | 1/10 | 2 | P1 | ||
DLGAP3 | ENST00000495979.1 | n.388C>A | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000313 AC: 64AN: 204670Hom.: 0 AF XY: 0.000351 AC XY: 39AN XY: 111250
GnomAD4 exome AF: 0.000109 AC: 157AN: 1440734Hom.: 2 Cov.: 33 AF XY: 0.000102 AC XY: 73AN XY: 714466
GnomAD4 genome AF: 0.000184 AC: 28AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 17, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at