chr13-95589176-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198968.4(DZIP1):c.2005C>T(p.Pro669Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,454,126 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_198968.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DZIP1 | NM_198968.4 | c.2005C>T | p.Pro669Ser | missense_variant | 19/23 | ENST00000376829.7 | NP_945319.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DZIP1 | ENST00000376829.7 | c.2005C>T | p.Pro669Ser | missense_variant | 19/23 | 1 | NM_198968.4 | ENSP00000366025.2 | ||
DZIP1 | ENST00000361396.6 | c.1948C>T | p.Pro650Ser | missense_variant | 18/22 | 1 | ENSP00000355175.2 | |||
DZIP1 | ENST00000347108.7 | c.2005C>T | p.Pro669Ser | missense_variant | 17/21 | 5 | ENSP00000257312.5 | |||
DZIP1 | ENST00000361156.7 | c.1948C>T | p.Pro650Ser | missense_variant | 16/20 | 5 | ENSP00000355018.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000409 AC: 1AN: 244352Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131900
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1454126Hom.: 0 Cov.: 29 AF XY: 0.00000277 AC XY: 2AN XY: 722932
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.2005C>T (p.P669S) alteration is located in exon 19 (coding exon 16) of the DZIP1 gene. This alteration results from a C to T substitution at nucleotide position 2005, causing the proline (P) at amino acid position 669 to be replaced by a serine (S). 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