rs6830513
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_181808.4(POLN):āc.1134A>Gā(p.Thr378=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,611,502 control chromosomes in the GnomAD database, including 24,710 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: š 0.25 ( 7155 hom., cov: 32)
Exomes š: 0.13 ( 17555 hom. )
Consequence
POLN
NM_181808.4 synonymous
NM_181808.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.36
Genes affected
POLN (HGNC:18870): (DNA polymerase nu) This gene encodes a DNA polymerase type-A family member. The encoded protein plays a role in DNA repair and homologous recombination. This gene shares its 5' exons with some transcripts from overlapping GeneID: 79441, which encodes an augmentin-like protein complex subunit. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP7
?
Synonymous conserved (PhyloP=-1.37 with no splicing effect.
BA1
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GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POLN | NM_181808.4 | c.1134A>G | p.Thr378= | synonymous_variant | 8/26 | ENST00000511885.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLN | ENST00000511885.6 | c.1134A>G | p.Thr378= | synonymous_variant | 8/26 | 5 | NM_181808.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.246 AC: 37469AN: 152066Hom.: 7137 Cov.: 32
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GnomAD3 exomes AF: 0.186 AC: 46810AN: 251210Hom.: 6259 AF XY: 0.174 AC XY: 23634AN XY: 135808
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GnomAD4 exome AF: 0.129 AC: 188416AN: 1459318Hom.: 17555 Cov.: 32 AF XY: 0.129 AC XY: 93331AN XY: 726144
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GnomAD4 genome ? AF: 0.247 AC: 37539AN: 152184Hom.: 7155 Cov.: 32 AF XY: 0.245 AC XY: 18201AN XY: 74410
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at