chr6-43516985-C-CGGG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The ENST00000646188.1(POLR1C):c.-96-318_-96-316dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 1,251,552 control chromosomes in the GnomAD database, including 306 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.015 ( 25 hom., cov: 32)
Exomes 𝑓: 0.019 ( 281 hom. )
Consequence
POLR1C
ENST00000646188.1 intron
ENST00000646188.1 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.38
Genes affected
POLR1C (HGNC:20194): (RNA polymerase I and III subunit C) The protein encoded by this gene is a subunit of both RNA polymerase I and RNA polymerase III complexes. The encoded protein is part of the Pol core element. Mutations in this gene have been associated with Treacher Collins syndrome (TCS) and hypomyelinating leukodystrophy 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 6-43516985-C-CGGG is Benign according to our data. Variant chr6-43516985-C-CGGG is described in ClinVar as [Likely_benign]. Clinvar id is 2580819.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.015 (2264/151386) while in subpopulation SAS AF= 0.0332 (160/4824). AF 95% confidence interval is 0.029. There are 25 homozygotes in gnomad4. There are 1053 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 25 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLR1C | ENST00000428025.6 | c.-96-318_-96-316dup | intron_variant | 4 | |||||
POLR1C | ENST00000646188.1 | c.-96-318_-96-316dup | intron_variant | ||||||
YIPF3 | ENST00000503972.5 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0150 AC: 2263AN: 151272Hom.: 25 Cov.: 32
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GnomAD4 exome AF: 0.0186 AC: 20464AN: 1100166Hom.: 281 Cov.: 15 AF XY: 0.0192 AC XY: 10778AN XY: 562100
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GnomAD4 genome ? AF: 0.0150 AC: 2264AN: 151386Hom.: 25 Cov.: 32 AF XY: 0.0142 AC XY: 1053AN XY: 74052
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 02, 2019 | See Variant Classification Assertion Criteria. - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at