17-28357347-G-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_015584.5(POLDIP2):c.102C>T(p.Ala34Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,573,656 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0068 ( 14 hom., cov: 33)
Exomes 𝑓: 0.00061 ( 16 hom. )
Consequence
POLDIP2
NM_015584.5 synonymous
NM_015584.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.284
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 17-28357347-G-A is Benign according to our data. Variant chr17-28357347-G-A is described in ClinVar as [Benign]. Clinvar id is 789657.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.284 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00684 (1042/152326) while in subpopulation AFR AF= 0.0239 (994/41580). AF 95% confidence interval is 0.0227. There are 14 homozygotes in gnomad4. There are 502 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 14 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POLDIP2 | ENST00000540200.6 | c.102C>T | p.Ala34Ala | synonymous_variant | Exon 1 of 11 | 1 | NM_015584.5 | ENSP00000475924.2 | ||
POLDIP2 | ENST00000618887.2 | c.102C>T | p.Ala34Ala | synonymous_variant | Exon 1 of 11 | 2 | ENSP00000477665.2 |
Frequencies
GnomAD3 genomes AF: 0.00684 AC: 1041AN: 152208Hom.: 14 Cov.: 33
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GnomAD3 exomes AF: 0.00163 AC: 219AN: 134698Hom.: 6 AF XY: 0.00126 AC XY: 98AN XY: 77968
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GnomAD4 exome AF: 0.000607 AC: 863AN: 1421330Hom.: 16 Cov.: 32 AF XY: 0.000501 AC XY: 354AN XY: 706734
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GnomAD4 genome AF: 0.00684 AC: 1042AN: 152326Hom.: 14 Cov.: 33 AF XY: 0.00674 AC XY: 502AN XY: 74496
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at