chr1-168729170-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001937.5(DPT):c.5A>C(p.Asp2Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 1,612,086 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 Likely benign (★).
Frequency
Consequence
NM_001937.5 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 | UniProt |
---|---|---|---|---|---|---|---|
DPT | NM_001937.5 | c.5A>C | p.Asp2Ala | missense_variant | 1/4 | ENST00000367817.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPT | ENST00000367817.4 | c.5A>C | p.Asp2Ala | missense_variant | 1/4 | 1 | NM_001937.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000786 AC: 196AN: 249346Hom.: 0 AF XY: 0.000579 AC XY: 78AN XY: 134798
GnomAD4 exome AF: 0.000147 AC: 215AN: 1459794Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 88AN XY: 725868
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at