Variant rs3824999 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006591.3(POLD3):c.1007-78T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 804,116 control chromosomes in the GnomAD database, including 87,844 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.40 ( 13753 hom., cov: 31)

Exomes 𝑓: 0.47 ( 74091 hom. )

Consequence

POLD3
NM_006591.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0740

Variant links:

Genes affected

POLD3 (HGNC:20932): (DNA polymerase delta 3, accessory subunit) This gene encodes the 66-kDa 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. The encoded protein plays a role in regulating the activity of DNA polymerase delta through interactions with other subunits and the processivity cofactor proliferating cell nuclear antigen (PCNA). Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Mar 2012]

POLD3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLD3	NM_006591.3 linkuse as main transcript	c.1007-78T>G		intron_variant		ENST00000263681.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLD3	ENST00000263681.7 linkuse as main transcript	c.1007-78T>G		intron_variant		1	NM_006591.3	P1	Q15054-1

Frequencies

GnomAD3 genomes

AF:

0.399

AC:

60678

AN:

151920

Hom.:

13758

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.547

Gnomad AMR

AF:

0.403

Gnomad ASJ

AF:

0.618

Gnomad EAS

AF:

0.400

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.492

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.511

Gnomad OTH

AF:

0.421

GnomAD4 exome

AF:

0.468

AC:

305188

AN:

652078

Hom.:

74091

AF XY:

0.467

AC XY:

163121

AN XY:

349386

show subpopulations

Gnomad4 AFR exome

AF:

0.172

Gnomad4 AMR exome

AF:

0.337

Gnomad4 ASJ exome

AF:

0.604

Gnomad4 EAS exome

AF:

0.414

Gnomad4 SAS exome

AF:

0.354

Gnomad4 FIN exome

AF:

0.489

Gnomad4 NFE exome

AF:

0.510

Gnomad4 OTH exome

AF:

0.464

GnomAD4 genome

AF:

0.399

AC:

60686

AN:

152038

Hom.:

13753

Cov.:

AF XY:

0.399

AC XY:

29642

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.175

Gnomad4 AMR

AF:

0.402

Gnomad4 ASJ

AF:

0.618

Gnomad4 EAS

AF:

0.401

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.492

Gnomad4 NFE

AF:

0.511

Gnomad4 OTH

AF:

0.417

Alfa

AF:

0.487

Hom.:

18389

Bravo

AF:

0.381

Asia WGS

AF:

0.333

AC:

1161

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.5

DANN

Benign

0.62

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over