7-87907796-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_006716.4(DBF4):c.1658C>T(p.Thr553Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000238 in 1,598,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006716.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DBF4 | NM_006716.4 | c.1658C>T | p.Thr553Ile | missense_variant | 12/12 | ENST00000265728.6 | |
DBF4 | NM_001318061.2 | c.986C>T | p.Thr329Ile | missense_variant | 12/12 | ||
DBF4 | NM_001318060.2 | c.959C>T | p.Thr320Ile | missense_variant | 11/11 | ||
DBF4 | NM_001318062.2 | c.878C>T | p.Thr293Ile | missense_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DBF4 | ENST00000265728.6 | c.1658C>T | p.Thr553Ile | missense_variant | 12/12 | 1 | NM_006716.4 | P1 | |
DBF4 | ENST00000413643.5 | c.*892C>T | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 1 | ||||
DBF4 | ENST00000431138.5 | c.*1431C>T | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000662 AC: 1AN: 150980Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250584Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135518
GnomAD4 exome AF: 0.0000256 AC: 37AN: 1447034Hom.: 0 Cov.: 31 AF XY: 0.0000167 AC XY: 12AN XY: 720016
GnomAD4 genome AF: 0.00000662 AC: 1AN: 150980Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73640
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.1658C>T (p.T553I) alteration is located in exon 12 (coding exon 12) of the DBF4 gene. This alteration results from a C to T substitution at nucleotide position 1658, causing the threonine (T) at amino acid position 553 to be replaced by an isoleucine (I). 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