Genetic Variant POLD1:p.Thr495Thr (chr19-50406508-C-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001308632.1(POLD1):c.1485C>T(p.Thr495Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,580,166 control chromosomes in the GnomAD database, including 11,895 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T495T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.099 ( 966 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10929 hom. )

Consequence

POLD1
NM_001308632.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: -5.27

Publications

19 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):

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: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp
mandibular hypoplasia-deafness-progeroid syndrome
Inheritance: AD, AR Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Genomics England PanelApp, Ambry Genetics, Orphanet, G2P
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

POLD1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 19-50406508-C-T is Benign according to our data. Variant chr19-50406508-C-T is described in ClinVar as Benign. ClinVar VariationId is 258787.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-5.27 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001308632.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
POLD1	NM_002691.4	MANE Select	c.1485C>T	p.Thr495Thr	synonymous	Exon 12 of 27	NP_002682.2
POLD1	NM_001308632.1		c.1485C>T	p.Thr495Thr	synonymous	Exon 11 of 26	NP_001295561.1
POLD1	NM_001256849.1		c.1485C>T	p.Thr495Thr	synonymous	Exon 12 of 27	NP_001243778.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
POLD1	ENST00000440232.7	TSL:1 MANE Select	c.1485C>T	p.Thr495Thr	synonymous	Exon 12 of 27	ENSP00000406046.1
POLD1	ENST00000595904.6	TSL:1	c.1485C>T	p.Thr495Thr	synonymous	Exon 12 of 27	ENSP00000472445.1
POLD1	ENST00000599857.7	TSL:1	c.1485C>T	p.Thr495Thr	synonymous	Exon 12 of 27	ENSP00000473052.1

Frequencies

GnomAD3 genomes

AF:

0.0987

AC:

15005

AN:

152050

Hom.:

964

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0411

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.0853

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.00847

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.117

GnomAD2 exomes

AF:

0.105

AC:

20740

AN:

198334

AF XY:

0.109

show subpopulations

Gnomad AFR exome

AF:

0.0340

Gnomad AMR exome

AF:

0.0585

Gnomad ASJ exome

AF:

0.171

Gnomad EAS exome

AF:

0.0122

Gnomad FIN exome

AF:

0.167

Gnomad NFE exome

AF:

0.115

Gnomad OTH exome

AF:

0.116

GnomAD4 exome

AF:

0.119

AC:

169994

AN:

1427996

Hom.:

10929

Cov.:

AF XY:

0.120

AC XY:

84765

AN XY:

707616

show subpopulations

African (AFR)

AF:

0.0393

AC:

1286

AN:

32694

American (AMR)

AF:

0.0620

AC:

2502

AN:

40356

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

4418

AN:

25494

East Asian (EAS)

AF:

0.00795

AC:

302

AN:

37982

South Asian (SAS)

AF:

0.140

AC:

11530

AN:

82218

European-Finnish (FIN)

AF:

0.162

AC:

8256

AN:

50946

Middle Eastern (MID)

AF:

0.138

AC:

724

AN:

5228

European-Non Finnish (NFE)

AF:

0.122

AC:

133723

AN:

1094024

Other (OTH)

AF:

0.123

AC:

7253

AN:

59054

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

7543

15085

22628

30170

37713

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4790

9580

14370

19160

23950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0987

AC:

15013

AN:

152170

Hom.:

966

Cov.:

AF XY:

0.100

AC XY:

7449

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.0411

AC:

1707

AN:

41512

American (AMR)

AF:

0.0852

AC:

1302

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

599

AN:

3468

East Asian (EAS)

AF:

0.00829

AC:

AN:

5186

South Asian (SAS)

AF:

0.137

AC:

663

AN:

4830

European-Finnish (FIN)

AF:

0.170

AC:

1796

AN:

10594

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.124

AC:

8441

AN:

67974

Other (OTH)

AF:

0.118

AC:

250

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

679

1357

2036

2714

3393

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<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:

0.104

Hom.:

1043

Bravo

AF:

0.0890

Asia WGS

AF:

0.0770

AC:

265

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (4)

Colorectal cancer, susceptibility to, 10 (3)

Hereditary cancer-predisposing syndrome (2)

not provided (2)

Mandibular hypoplasia-deafness-progeroid syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

2.9

(source)

DANN

Benign

0.61

PhyloP100

-5.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.9

Mutation Taster

=97/3

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over