2-26402025-G-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_145038.5(DRC1):āc.36G>Cā(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 (ā ā ).
Frequency
Genomes: š 0.0087 ( 18 hom., cov: 32)
Exomes š: 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 GnomAd4 at 18 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DRC1 | NM_145038.5 | c.36G>C | p.Pro12= | synonymous_variant | 1/17 | ENST00000288710.7 | NP_659475.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DRC1 | ENST00000288710.7 | c.36G>C | p.Pro12= | synonymous_variant | 1/17 | 2 | NM_145038.5 | ENSP00000288710 | P1 | |
DRC1 | ENST00000421869.5 | c.36G>C | p.Pro12= | synonymous_variant, NMD_transcript_variant | 1/8 | 1 | ENSP00000414375 | |||
DRC1 | ENST00000649059.1 | c.24G>C | p.Pro8= | synonymous_variant, NMD_transcript_variant | 1/16 | ENSP00000497543 |
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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GnomAD4 genome AF: 0.00874 AC: 1332AN: 152326Hom.: 18 Cov.: 32 AF XY: 0.00861 AC XY: 641AN XY: 74480
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
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 | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Primary ciliary dyskinesia 21 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 03, 2022 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at