chr10-101579385-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001174084.2(POLL):c.*68C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 1,513,876 control chromosomes in the GnomAD database, including 4,304 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.076 ( 479 hom., cov: 32)
Exomes 𝑓: 0.072 ( 3825 hom. )
Consequence
POLL
NM_001174084.2 3_prime_UTR
NM_001174084.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.163
Genes affected
POLL (HGNC:9184): (DNA polymerase lambda) This gene encodes a DNA polymerase. DNA polymerases catalyze DNA-template-directed extension of the 3'-end of a DNA strand. This particular polymerase, which is a member of the X family of DNA polymerases, likely plays a role in non-homologous end joining and other DNA repair processes. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2010]
DPCD (HGNC:24542): (deleted in primary ciliary dyskinesia homolog (mouse)) This gene in mouse encodes a protein that may be involved in the generation and maintenance of ciliated cells. In mouse, expression of this gene increases during ciliated cell differentiation, and disruption of this gene has been linked to primary ciliary dyskinesia. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 10-101579385-G-A is Benign according to our data. Variant chr10-101579385-G-A is described in ClinVar as [Benign]. Clinvar id is 1279768.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POLL | NM_001174084.2 | c.*68C>T | 3_prime_UTR_variant | 9/9 | ENST00000370162.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLL | ENST00000370162.8 | c.*68C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_001174084.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0762 AC: 11591AN: 152032Hom.: 477 Cov.: 32
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GnomAD4 exome AF: 0.0723 AC: 98454AN: 1361726Hom.: 3825 Cov.: 29 AF XY: 0.0715 AC XY: 47927AN XY: 670750
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GnomAD4 genome ? AF: 0.0763 AC: 11608AN: 152150Hom.: 479 Cov.: 32 AF XY: 0.0741 AC XY: 5509AN XY: 74386
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at