chr7-154053046-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_130797.4(DPP6):c.226G>A(p.Asp76Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0226 in 1,058,538 control chromosomes in the GnomAD database, including 312 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 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. D76V) has been classified as Likely benign.
Frequency
Consequence
NM_130797.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPP6 | NM_130797.4 | c.226G>A | p.Asp76Asn | missense_variant | 1/26 | ENST00000377770.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPP6 | ENST00000377770.8 | c.226G>A | p.Asp76Asn | missense_variant | 1/26 | 1 | NM_130797.4 | ||
DPP6 | ENST00000406326.5 | c.226G>A | p.Asp76Asn | missense_variant | 1/6 | 1 | |||
DPP6 | ENST00000404039.5 | c.51+165312G>A | intron_variant | 1 | |||||
DPP6 | ENST00000706130.1 | c.60+304038G>A | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.0161 AC: 2406AN: 149792Hom.: 26 Cov.: 31
GnomAD3 exomes AF: 0.0286 AC: 63AN: 2200Hom.: 0 AF XY: 0.0297 AC XY: 39AN XY: 1312
GnomAD4 exome AF: 0.0237 AC: 21490AN: 908634Hom.: 286 Cov.: 37 AF XY: 0.0236 AC XY: 10017AN XY: 424422
GnomAD4 genome AF: 0.0161 AC: 2407AN: 149904Hom.: 26 Cov.: 31 AF XY: 0.0171 AC XY: 1253AN XY: 73148
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 10, 2016 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at