19-50384344-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001256849.1(POLD1):c.-51G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00378 in 152,616 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001256849.1 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POLD1 | NM_002691.4 | c.-48G>A | upstream_gene_variant | ENST00000440232.7 | NP_002682.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00376 AC: 573AN: 152224Hom.: 5 Cov.: 33
GnomAD4 exome AF: 0.0182 AC: 5AN: 274Hom.: 0 Cov.: 0 AF XY: 0.0140 AC XY: 3AN XY: 214
GnomAD4 genome AF: 0.00375 AC: 572AN: 152342Hom.: 5 Cov.: 33 AF XY: 0.00356 AC XY: 265AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:2
POLD1: BS1, BS2 -
- -
not specified Benign: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. -
Colorectal cancer, susceptibility to, 10 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at