16-30429959-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024096.2(DCTPP1):c.22A>T(p.Ile8Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000197 in 1,576,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024096.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCTPP1 | ENST00000319285.5 | c.22A>T | p.Ile8Phe | missense_variant | 1/3 | 1 | NM_024096.2 | ENSP00000322524.4 | ||
ZNF771 | ENST00000566625.2 | c.*1062T>A | 3_prime_UTR_variant | 3/3 | 1 | ENSP00000460549.1 | ||||
DCTPP1 | ENST00000567983.1 | c.22A>T | p.Ile8Phe | missense_variant | 1/2 | 5 | ENSP00000456612.1 | |||
DCTPP1 | ENST00000565758.1 | c.-367A>T | 5_prime_UTR_variant | 1/3 | 3 | ENSP00000460933.1 |
Frequencies
GnomAD3 genomes AF: 0.0000791 AC: 12AN: 151758Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000960 AC: 2AN: 208244Hom.: 0 AF XY: 0.00000871 AC XY: 1AN XY: 114820
GnomAD4 exome AF: 0.0000133 AC: 19AN: 1424644Hom.: 0 Cov.: 30 AF XY: 0.00000988 AC XY: 7AN XY: 708180
GnomAD4 genome AF: 0.0000791 AC: 12AN: 151758Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74096
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.22A>T (p.I8F) alteration is located in exon 1 (coding exon 1) of the DCTPP1 gene. This alteration results from a A to T substitution at nucleotide position 22, causing the isoleucine (I) at amino acid position 8 to be replaced by a phenylalanine (F). 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