GeneBe

rs35689550

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_002691.4(POLD1):​c.-1-272_-1-259delAAAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000016 ( 0 hom., cov: 0)

Consequence

POLD1
NM_002691.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.549

Publications

0 publications found
Variant links:
Genes affected
POLD1 (HGNC:9175): (DNA polymerase delta 1, catalytic subunit) This gene encodes the 125-kDa catalytic subunit of DNA polymerase delta. DNA polymerase delta possesses both polymerase and 3' to 5' exonuclease activity and plays a critical role in DNA replication and repair. Alternatively spliced transcript variants have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 6. [provided by RefSeq, Mar 2012]
POLD1 Gene-Disease associations (from GenCC):
  • mandibular hypoplasia-deafness-progeroid syndrome
    Inheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen, Genomics England PanelApp
  • POLD1-related polyposis and colorectal cancer syndrome
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
  • colorectal cancer, susceptibility to, 10
    Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
  • Polymerase proofreading-related adenomatous polyposis
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • immunodeficiency 120
    Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
  • non-severe combined immunodeficiency due to polymerase delta deficiency
    Inheritance: AR Classification: LIMITED Submitted by: ClinGen

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002691.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
POLD1
NM_002691.4
MANE Select
c.-1-272_-1-259delAAAAAAAAAAAAAA
intron
N/ANP_002682.2P28340
POLD1
NM_001256849.1
c.-4-269_-4-256delAAAAAAAAAAAAAA
intron
N/ANP_001243778.1P28340
POLD1
NM_001438212.1
c.-1-272_-1-259delAAAAAAAAAAAAAA
intron
N/ANP_001425141.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
POLD1
ENST00000440232.7
TSL:1 MANE Select
c.-1-280_-1-267delAAAAAAAAAAAAAA
intron
N/AENSP00000406046.1P28340
POLD1
ENST00000595904.6
TSL:1
c.-1-280_-1-267delAAAAAAAAAAAAAA
intron
N/AENSP00000472445.1M0R2B7
POLD1
ENST00000599857.7
TSL:1
c.-4-277_-4-264delAAAAAAAAAAAAAA
intron
N/AENSP00000473052.1P28340

Frequencies

GnomAD3 genomes
AF:
0.0000156
AC:
1
AN:
64220
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000258
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000156
AC:
1
AN:
64220
Hom.:
0
Cov.:
0
AF XY:
0.0000367
AC XY:
1
AN XY:
27266
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
14544
American (AMR)
AF:
0.00
AC:
0
AN:
4098
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2150
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1718
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1054
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
510
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
58
European-Non Finnish (NFE)
AF:
0.0000258
AC:
1
AN:
38804
Other (OTH)
AF:
0.00
AC:
0
AN:
744
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs35689550; hg19: chr19-50901827; API