rs746939507
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_145038.5(DRC1):c.15G>A(p.Gly5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000151 in 1,607,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 0 hom. )
Consequence
DRC1
NM_145038.5 synonymous
NM_145038.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.190
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
?
Variant 2-26402004-G-A is Benign according to our data. Variant chr2-26402004-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 241935.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.19 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DRC1 | NM_145038.5 | c.15G>A | p.Gly5= | synonymous_variant | 1/17 | ENST00000288710.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DRC1 | ENST00000288710.7 | c.15G>A | p.Gly5= | synonymous_variant | 1/17 | 2 | NM_145038.5 | P1 | |
DRC1 | ENST00000421869.5 | c.15G>A | p.Gly5= | synonymous_variant, NMD_transcript_variant | 1/8 | 1 | |||
DRC1 | ENST00000649059.1 | c.3G>A | p.Ter1= | coding_sequence_variant, NMD_transcript_variant | 1/16 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152232Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000843 AC: 20AN: 237130Hom.: 0 AF XY: 0.0000932 AC XY: 12AN XY: 128776
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GnomAD4 exome AF: 0.000161 AC: 235AN: 1455692Hom.: 0 Cov.: 30 AF XY: 0.000158 AC XY: 114AN XY: 723496
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74372
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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 | Invitae | Oct 05, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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