22-42585834-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032311.5(POLDIP3):c.1223C>T(p.Ala408Val) variant causes a missense change. The variant allele was found at a frequency of 0.000107 in 1,612,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032311.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POLDIP3 | ENST00000252115.10 | c.1223C>T | p.Ala408Val | missense_variant | Exon 9 of 9 | 1 | NM_032311.5 | ENSP00000252115.5 | ||
ENSG00000289517 | ENST00000617178.5 | n.*2084C>T | non_coding_transcript_exon_variant | Exon 14 of 14 | 1 | ENSP00000482500.2 | ||||
ENSG00000289517 | ENST00000617178.5 | n.*2084C>T | 3_prime_UTR_variant | Exon 14 of 14 | 1 | ENSP00000482500.2 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251304Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135842
GnomAD4 exome AF: 0.000110 AC: 160AN: 1460674Hom.: 0 Cov.: 30 AF XY: 0.0000922 AC XY: 67AN XY: 726672
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1223C>T (p.A408V) alteration is located in exon 9 (coding exon 9) of the POLDIP3 gene. This alteration results from a C to T substitution at nucleotide position 1223, causing the alanine (A) at amino acid position 408 to be replaced by a valine (V). 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