chr2-26402025-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_145038.5(DRC1):c.36G>C(p.Pro12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00165 in 1,612,076 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0087 ( 18 hom., cov: 32)
Exomes 𝑓: 0.00091 ( 16 hom. )
Consequence
DRC1
NM_145038.5 synonymous
NM_145038.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.335
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
Variant 2-26402025-G-C is Benign according to our data. Variant chr2-26402025-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 241940.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.335 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00874 (1332/152326) while in subpopulation AFR AF= 0.0306 (1270/41568). AF 95% confidence interval is 0.0292. There are 18 homozygotes in gnomad4. There are 641 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 18 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DRC1 | NM_145038.5 | c.36G>C | p.Pro12= | synonymous_variant | 1/17 | ENST00000288710.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DRC1 | ENST00000288710.7 | c.36G>C | p.Pro12= | synonymous_variant | 1/17 | 2 | NM_145038.5 | P1 | |
DRC1 | ENST00000421869.5 | c.36G>C | p.Pro12= | synonymous_variant, NMD_transcript_variant | 1/8 | 1 | |||
DRC1 | ENST00000649059.1 | c.24G>C | p.Pro8= | synonymous_variant, NMD_transcript_variant | 1/16 |
Frequencies
GnomAD3 genomes ? AF: 0.00872 AC: 1327AN: 152208Hom.: 18 Cov.: 32
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GnomAD3 exomes AF: 0.00223 AC: 547AN: 245552Hom.: 7 AF XY: 0.00160 AC XY: 214AN XY: 133340
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GnomAD4 exome AF: 0.000912 AC: 1332AN: 1459750Hom.: 16 Cov.: 30 AF XY: 0.000788 AC XY: 572AN XY: 725928
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Primary ciliary dyskinesia 21 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 03, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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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