rs1054737
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_145038.5(DRC1):c.*9G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 1,613,910 control chromosomes in the GnomAD database, including 3,534 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.046 ( 213 hom., cov: 33)
Exomes 𝑓: 0.063 ( 3321 hom. )
Consequence
DRC1
NM_145038.5 3_prime_UTR
NM_145038.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.830
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 2-26456526-G-A is Benign according to our data. Variant chr2-26456526-G-A is described in ClinVar as [Benign]. Clinvar id is 262563.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.064 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DRC1 | NM_145038.5 | c.*9G>A | 3_prime_UTR_variant | 17/17 | ENST00000288710.7 | NP_659475.2 | ||
DRC1 | XM_047446339.1 | c.*9G>A | 3_prime_UTR_variant | 10/10 | XP_047302295.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DRC1 | ENST00000288710.7 | c.*9G>A | 3_prime_UTR_variant | 17/17 | 2 | NM_145038.5 | ENSP00000288710.2 | |||
DRC1 | ENST00000649059.1 | n.*1195G>A | non_coding_transcript_exon_variant | 16/16 | ENSP00000497543.1 | |||||
DRC1 | ENST00000649059.1 | n.*1195G>A | 3_prime_UTR_variant | 16/16 | ENSP00000497543.1 |
Frequencies
GnomAD3 genomes AF: 0.0462 AC: 7038AN: 152204Hom.: 213 Cov.: 33
GnomAD3 genomes
AF:
AC:
7038
AN:
152204
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0436 AC: 10962AN: 251272Hom.: 303 AF XY: 0.0449 AC XY: 6092AN XY: 135814
GnomAD3 exomes
AF:
AC:
10962
AN:
251272
Hom.:
AF XY:
AC XY:
6092
AN XY:
135814
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0628 AC: 91745AN: 1461590Hom.: 3321 Cov.: 31 AF XY: 0.0613 AC XY: 44592AN XY: 727086
GnomAD4 exome
AF:
AC:
91745
AN:
1461590
Hom.:
Cov.:
31
AF XY:
AC XY:
44592
AN XY:
727086
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0462 AC: 7039AN: 152320Hom.: 213 Cov.: 33 AF XY: 0.0433 AC XY: 3223AN XY: 74480
GnomAD4 genome
AF:
AC:
7039
AN:
152320
Hom.:
Cov.:
33
AF XY:
AC XY:
3223
AN XY:
74480
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
53
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
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 - |
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at