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NM_002691.4:c.2953C>T
p.Arg985Trp · POLD1
ACMG/AMP
0%
complete
Final classification
VUS
PM2
POLD1
c.2953C>T
p.Arg985Trp
This variant

The POLD1 c.2953C>T (p.Arg985Trp) variant has been reported in ClinVar as a variant of uncertain significance by five clinical laboratories.

Transcript
NM_002691.4
HGVS · transcript:coding
NM_002691.4:c.2953C>T
GRCh38
chr19:50416528 C>T
GRCh37
chr19:50919785 C>T
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate; combination = 1 moderate, which maps to VUS.
Classification rationale
PM2 VUS
POLD1 c.2953C>T

The POLD1 c.2953C>T (p.Arg985Trp) variant has been reported in ClinVar as a variant of uncertain significance by five clinical laboratories.1 This variant is present at very low frequency in population databases, with gnomAD v2.1 AF 1.07182e-05 (2/186598) and gnomAD v4.1 AF 5.15439e-06 (8/1552074), both below the 0.1% PM2 threshold.2 Computational evidence is conflicting: SpliceAI predicts possible splice impact with a max delta score of 0.59, whereas REVEL is low at 0.126 and BayesDel is -0.414351, so PP3 and BP4 are not applied.3

PM2 VUS
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Gene diagram · NM_002691.4 · variants mapped to exon structure
POLD1 NM_002691.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 22 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
This variant is present at very low frequency in population databases and remains below the non-VCEP PM2 threshold of 0.1% in both datasets reviewed: gnomAD v2.1 AF 1.07182e-05 (0.00107%, 2/186598) and gnomAD v4.1 AF 5.15439e-06 (0.00052%, 8/1552074). This supports PM2.
gnomAD v2.1 AF 1.07182e-05gnomAD v4.1 AF 5.15439e-06
Assessed · not applied · 7 not met · 15 not assessed
Pathogenic
PS1 No reviewed evidence identified another nucleotide change causing the same amino acid substitution with an established pathogenic classification, so PS1 cannot be assessed from the available evidence.
PS2 No confirmed de novo occurrence with parental confirmation was identified for this variant, so PS2 is not assessed.
PS3 No well-established functional study showing a damaging effect of p.(Arg985Trp) was identified, so PS3 is not assessed.
PS4 No case-control enrichment or affected-individual series demonstrating a significant excess of this variant in disease was identified, so PS4 is not assessed.
PM1 This residue was not identified in Cancer Hotspots, and available reviewed evidence does not show that p.Arg985 lies in a statistically significant hotspot for this gene.
PM5 No reviewed evidence identified a different pathogenic missense change at the same amino acid residue, so PM5 is not assessed.
PM6 No apparent de novo report without full parental confirmation was identified for this variant, so PM6 is not assessed.
PP1 No segregation data were identified for this variant, so PP1 is not assessed.
PP2 Available reviewed sources do not establish a gene-level missense pattern that would support PP2 for this variant, so PP2 is not assessed.
PP3 Computational evidence is conflicting rather than consistently damaging.
PP4 No individual-level phenotype or family history data were provided that would support a highly specific clinical presentation for this variant, so PP4 is not assessed.
PP5 ClinVar lists this variant as Uncertain significance with single-submitter review status rather than as a pathogenic or likely pathogenic expert classification, so PP5 is not met.
Benign
BA1 Population frequency does not meet the benign stand-alone threshold of 1%.
BS1 Population frequency does not exceed the non-VCEP BS1 threshold of 0.3%.
BS2 Available reviewed evidence does not document this variant in a sufficient number of unaffected adults for the relevant disorder context, so BS2 is not assessed.
BS3 No well-established functional study showing a normal or non-damaging effect of p.(Arg985Trp) was identified, so BS3 is not assessed.
BS4 No non-segregation data were identified for this variant, so BS4 is not assessed.
BP1 Available reviewed evidence does not establish that missense variants in this gene are generally a poor mechanism of disease, so BP1 is not assessed.
BP2 No phase or co-occurrence data with another pathogenic variant were identified for this variant, so BP2 is not assessed.
BP4 Computational evidence does not consistently support a benign interpretation.
BP5 No alternate molecular explanation or independent cause for the phenotype was identified from the available evidence, so BP5 is not assessed.
BP6 ClinVar does not provide a benign or likely benign reputable-source classification for this variant; the reported classification is Uncertain significance, so BP6 is not met.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 5.15439e-06; MAF= 0.00052%, 8/1552074 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.554e-05; MAF= 0.00355%, 3/84412 alleles, homozygotes = 0); grpmax FAF= 9.44e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.07182e-05; MAF= 0.00107%, 2/186598 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 5.86441e-05; MAF= 0.00586%, 1/17052 alleles, homozygotes = 0).
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00052% · 8 / 1,552,074
0 hom · FAF 0.00094%
South Asian
3 / 84,412
0.0036%
African/African American
1 / 73,290
0.0014%
European (non-Finnish)
4 / 1,149,942
0.00035%
+ 7 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish)
gnomAD v2.1
0.0011% · 2 / 186,598
0 hom
African/African American
1 / 17,052
0.0059%
South Asian
1 / 23,132
0.0043%
+ 6 not observed (Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals)
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (5 clinical laboratories).
SpliceAI screenshot
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.59). REVEL score = 0.126. BayesDel score = -0.414351.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. POLD1, a DNA polymerase, is infrequently altered by mutation in cancer.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
Cancer hotspots