chr19-50415421-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_002691.4(POLD1):c.2565-17G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000514 in 1,604,110 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002691.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POLD1 | NM_002691.4 | c.2565-17G>A | intron_variant | Intron 20 of 26 | ENST00000440232.7 | NP_002682.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000729 AC: 111AN: 152172Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000777 AC: 191AN: 245866Hom.: 0 AF XY: 0.000784 AC XY: 105AN XY: 133966
GnomAD4 exome AF: 0.000491 AC: 713AN: 1451820Hom.: 2 Cov.: 32 AF XY: 0.000505 AC XY: 364AN XY: 720466
GnomAD4 genome AF: 0.000729 AC: 111AN: 152290Hom.: 2 Cov.: 33 AF XY: 0.000846 AC XY: 63AN XY: 74472
ClinVar
Submissions by phenotype
Colorectal cancer, susceptibility to, 10 Benign:3
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not specified Uncertain:1Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Uncertain:1Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at