Variant rs1054737 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.830

Variant links:

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]

DRC1 links:

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 linkuse as main transcript	c.*9G>A		3_prime_UTR_variant	17/17	ENST00000288710.7	NP_659475.2	Q96MC2
DRC1	XM_047446339.1 linkuse as main transcript	c.*9G>A		3_prime_UTR_variant	10/10		XP_047302295.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DRC1	ENST00000288710.7 linkuse as main transcript	c.*9G>A	3_prime_UTR_variant	17/17	2	NM_145038.5	ENSP00000288710.2	Q96MC2
DRC1	ENST00000649059.1 linkuse as main transcript	n.*1195G>A	non_coding_transcript_exon_variant	16/16			ENSP00000497543.1	A0A3B3IT12
DRC1	ENST00000649059.1 linkuse as main transcript	n.*1195G>A	3_prime_UTR_variant	16/16			ENSP00000497543.1	A0A3B3IT12

Frequencies

GnomAD3 genomes

AF:

0.0462

AC:

7038

AN:

152204

Hom.:

213

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0320

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.0339

Gnomad ASJ

AF:

0.0412

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0244

Gnomad FIN

AF:

0.0312

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0657

Gnomad OTH

AF:

0.0435

GnomAD3 exomes

AF:

0.0436

AC:

10962

AN:

251272

Hom.:

303

AF XY:

0.0449

AC XY:

6092

AN XY:

135814

show subpopulations

Gnomad AFR exome

AF:

0.0321

Gnomad AMR exome

AF:

0.0243

Gnomad ASJ exome

AF:

0.0401

Gnomad EAS exome

AF:

0.000381

Gnomad SAS exome

AF:

0.0247

Gnomad FIN exome

AF:

0.0341

Gnomad NFE exome

AF:

0.0651

Gnomad OTH exome

AF:

0.0480

GnomAD4 exome

AF:

0.0628

AC:

91745

AN:

1461590

Hom.:

3321

Cov.:

AF XY:

0.0613

AC XY:

44592

AN XY:

727086

show subpopulations

Gnomad4 AFR exome

AF:

0.0286

Gnomad4 AMR exome

AF:

0.0248

Gnomad4 ASJ exome

AF:

0.0403

Gnomad4 EAS exome

AF:

0.00111

Gnomad4 SAS exome

AF:

0.0254

Gnomad4 FIN exome

AF:

0.0375

Gnomad4 NFE exome

AF:

0.0727

Gnomad4 OTH exome

AF:

0.0564

GnomAD4 genome

AF:

0.0462

AC:

7039

AN:

152320

Hom.:

213

Cov.:

AF XY:

0.0433

AC XY:

3223

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.0320

Gnomad4 AMR

AF:

0.0339

Gnomad4 ASJ

AF:

0.0412

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0244

Gnomad4 FIN

AF:

0.0312

Gnomad4 NFE

AF:

0.0656

Gnomad4 OTH

AF:

0.0435

Alfa

AF:

0.0577

Hom.:

410

Bravo

AF:

0.0463

Asia WGS

AF:

0.0140

AC:

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	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 -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.43

DANN

Benign

0.93

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over