chr19-50417158-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_002691.4(POLD1):c.3121-14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,586,784 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POLD1 | NM_002691.4 | c.3121-14G>A | intron_variant | Intron 25 of 26 | ENST00000440232.7 | NP_002682.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152074Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000135 AC: 28AN: 206784Hom.: 0 AF XY: 0.000116 AC XY: 13AN XY: 112170
GnomAD4 exome AF: 0.000114 AC: 164AN: 1434590Hom.: 0 Cov.: 33 AF XY: 0.000115 AC XY: 82AN XY: 711624
GnomAD4 genome AF: 0.000302 AC: 46AN: 152194Hom.: 0 Cov.: 34 AF XY: 0.000296 AC XY: 22AN XY: 74426
ClinVar
Submissions by phenotype
Colorectal cancer, susceptibility to, 10 Benign:2
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Hereditary cancer-predisposing syndrome Uncertain:1
The c.3121-14G>A intronic alteration consists of a G to A substitution 14 nucleotides before coding exon 25 in the POLD1 gene. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
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. -
Polymerase proofreading-related adenomatous polyposis Benign:1
The POLD1 c.3121-14G>A variant was not identified in the literature. The variant was identified in dbSNP (ID: rs367766963) as “With Likely benign allele” and ClinVar (classified as likely benign by GeneDx, PreventionGenetics and Counsyl). The variant was identified in control databases in 36 of 231642 chromosomes at a frequency of 0.0002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 15 of 20212 chromosomes (freq: 0.0007), Latino in 9 of 30460 chromosomes (freq: 0.0003), European Non-Finnish in 9 of 102726 chromosomes (freq: 0.00009), East Asian in 2 of 16182 chromosomes (freq: 0.0001), and South Asian in 1 of 27054 chromosomes (freq: 0.00004); it was not observed in the Other, Ashkenazi Jewish, or European Finnish populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at