17-28357257-GT-G

Variant names:

• chr17-28357257-GT-G
• rs11314852
• NM_015584.5:c.161+30delA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015584.5(POLDIP2):​c.161+30delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 1.0 (76160 hom., cov: 0)
  • Exomes 𝑓: 1.0 (700540 hom.)
• Consequence: POLDIP2 NM_015584.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0510
• Publications: 7 publications found

Genes affected

POLDIP2 (HGNC:23781): (DNA polymerase delta interacting protein 2) This gene encodes a protein that interacts with the DNA polymerase delta p50 subunit, as well as with proliferating cell nuclear antigen. The encoded protein maybe play a role in the ability of the replication fork to bypass DNA lesions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 17-28357257-GT-G is Benign according to our data. Variant chr17-28357257-GT-G is described in ClinVar as Benign. ClinVar VariationId is 1237395.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015584.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLDIP2	NM_015584.5	MANE Select	c.161+30delA		intron	N/A	NP_056399.1	Q9Y2S7
	POLDIP2	NM_001290145.2		c.161+30delA		intron	N/A	NP_001277074.1	B4DEM9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLDIP2	ENST00000540200.6	TSL:1 MANE Select	c.161+30delA		intron	N/A	ENSP00000475924.2	Q9Y2S7
	POLDIP2	ENST00000902298.1		c.161+30delA		intron	N/A	ENSP00000572357.1
	POLDIP2	ENST00000902300.1		c.161+30delA		intron	N/A	ENSP00000572359.1

Frequencies

GnomAD3 genomes AF: 1.00 AC: 152202 AN: 152202 Hom.: 76101 Cov.: 0

Gnomad AFR AF: 1.00

Gnomad AMI AF: 1.00

Gnomad AMR AF: 1.00

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 1.00

GnomAD2 exomes AF: 1.00 AC: 160478 AN: 160478 AF XY: 1.00

Gnomad AFR exome AF: 1.00

Gnomad AMR exome AF: 1.00

Gnomad ASJ exome AF: 1.00

Gnomad EAS exome AF: 1.00

Gnomad FIN exome AF: 1.00

Gnomad NFE exome AF: 1.00

Gnomad OTH exome AF: 1.00

GnomAD4 exome AF: 1.00 AC: 1401095 AN: 1401110 Hom.: 700540 Cov.: 0 AF XY: 1.00 AC XY: 696158 AN XY: 696164

African (AFR) AF: 1.00 AC: 29216 AN: 29218

American (AMR) AF: 1.00 AC: 40587 AN: 40588

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 24625 AN: 24626

East Asian (EAS) AF: 1.00 AC: 34210 AN: 34210

South Asian (SAS) AF: 1.00 AC: 81605 AN: 81606

European-Finnish (FIN) AF: 1.00 AC: 35884 AN: 35884

Middle Eastern (MID) AF: 1.00 AC: 4624 AN: 4624

European-Non Finnish (NFE) AF: 1.00 AC: 1092103 AN: 1092112

Other (OTH) AF: 1.00 AC: 58241 AN: 58242

GnomAD4 genome AF: 1.00 AC: 152320 AN: 152320 Hom.: 76160 Cov.: 0 AF XY: 1.00 AC XY: 74490 AN XY: 74490

African (AFR) AF: 1.00 AC: 41586 AN: 41586

American (AMR) AF: 1.00 AC: 15310 AN: 15310

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5168 AN: 5168

South Asian (SAS) AF: 1.00 AC: 4828 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10628 AN: 10628

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68010 AN: 68010

Other (OTH) AF: 1.00 AC: 2112 AN: 2112

Alfa AF: 0.999 Hom.: 12859

Asia WGS AF: 1.00 AC: 3478 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.051
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11314852; hg19: chr17-26684283;