rs878855222
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2
The NM_145038.5(DRC1):c.1720_1734delAAGGCGAGCATGGAG(p.Lys574_Glu578del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000312 in 1,614,126 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0018 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 2 hom. )
Consequence
DRC1
NM_145038.5 conservative_inframe_deletion
NM_145038.5 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.571
Genes affected
DRC1 (HGNC:24245): (dynein regulatory complex subunit 1) This gene encodes a central component of the nexin-dynein complex (N-DRC), which regulates the assembly of ciliary dynein. Mutations in this gene can cause ciliary dyskinesia. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_145038.5.
BP6
Variant 2-26453335-CAGGCGAGCATGGAGA-C is Benign according to our data. Variant chr2-26453335-CAGGCGAGCATGGAGA-C is described in ClinVar as [Likely_benign]. Clinvar id is 241936.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00177 (269/152300) while in subpopulation AFR AF= 0.00611 (254/41552). AF 95% confidence interval is 0.0055. There are 1 homozygotes in gnomad4. There are 133 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DRC1 | NM_145038.5 | c.1720_1734delAAGGCGAGCATGGAG | p.Lys574_Glu578del | conservative_inframe_deletion | 14/17 | ENST00000288710.7 | NP_659475.2 | |
DRC1 | XM_047446339.1 | c.700_714delAAGGCGAGCATGGAG | p.Lys234_Glu238del | conservative_inframe_deletion | 7/10 | XP_047302295.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DRC1 | ENST00000288710.7 | c.1720_1734delAAGGCGAGCATGGAG | p.Lys574_Glu578del | conservative_inframe_deletion | 14/17 | 2 | NM_145038.5 | ENSP00000288710.2 | ||
DRC1 | ENST00000439066.2 | n.450_464delAAGGCGAGCATGGAG | non_coding_transcript_exon_variant | 5/5 | 3 | |||||
DRC1 | ENST00000649059.1 | n.*683_*697delAAGGCGAGCATGGAG | non_coding_transcript_exon_variant | 13/16 | ENSP00000497543.1 | |||||
DRC1 | ENST00000649059.1 | n.*683_*697delAAGGCGAGCATGGAG | 3_prime_UTR_variant | 13/16 | ENSP00000497543.1 |
Frequencies
GnomAD3 genomes AF: 0.00175 AC: 267AN: 152182Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000442 AC: 110AN: 248928Hom.: 0 AF XY: 0.000371 AC XY: 50AN XY: 134746
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GnomAD4 exome AF: 0.000161 AC: 235AN: 1461826Hom.: 2 AF XY: 0.000110 AC XY: 80AN XY: 727214
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GnomAD4 genome AF: 0.00177 AC: 269AN: 152300Hom.: 1 Cov.: 32 AF XY: 0.00179 AC XY: 133AN XY: 74464
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 27, 2023 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at