Variant rs4072407 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.1397-15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 1,612,870 control chromosomes in the GnomAD database, including 496,994 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.66 ( 37103 hom., cov: 33)

Exomes 𝑓: 0.78 ( 459891 hom. )

Consequence

DRC1
NM_145038.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -2.30

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:

DRC1 (HGNC:):

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=-1.03).

BP6

Variant 2-26448676-A-G is Benign according to our data. Variant chr2-26448676-A-G is described in ClinVar as [Benign]. Clinvar id is 262565.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 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.1397-15A>G		intron_variant		ENST00000288710.7	NP_659475.2	Q96MC2
DRC1	XM_047446339.1 linkuse as main transcript	c.377-15A>G		intron_variant			XP_047302295.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
DRC1	ENST00000288710.7 linkuse as main transcript	c.1397-15A>G	intron_variant	2	NM_145038.5	ENSP00000288710.2	Q96MC2
DRC1	ENST00000439066.2 linkuse as main transcript	n.127-15A>G	intron_variant	3
DRC1	ENST00000649059.1 linkuse as main transcript	n.*360-15A>G	intron_variant			ENSP00000497543.1	A0A3B3IT12

Frequencies

GnomAD3 genomes

AF:

0.664

AC:

101014

AN:

152044

Hom.:

37097

Cov.:

show subpopulations

Gnomad AFR

AF:

0.375

Gnomad AMI

AF:

0.872

Gnomad AMR

AF:

0.629

Gnomad ASJ

AF:

0.821

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.723

Gnomad FIN

AF:

0.904

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.825

Gnomad OTH

AF:

0.695

GnomAD3 exomes

AF:

0.714

AC:

179396

AN:

251128

Hom.:

68744

AF XY:

0.733

AC XY:

99488

AN XY:

135756

show subpopulations

Gnomad AFR exome

AF:

0.357

Gnomad AMR exome

AF:

0.565

Gnomad ASJ exome

AF:

0.816

Gnomad EAS exome

AF:

0.266

Gnomad SAS exome

AF:

0.737

Gnomad FIN exome

AF:

0.903

Gnomad NFE exome

AF:

0.830

Gnomad OTH exome

AF:

0.768

GnomAD4 exome

AF:

0.783

AC:

1143533

AN:

1460708

Hom.:

459891

Cov.:

AF XY:

0.784

AC XY:

570023

AN XY:

726662

show subpopulations

Gnomad4 AFR exome

AF:

0.354

Gnomad4 AMR exome

AF:

0.576

Gnomad4 ASJ exome

AF:

0.808

Gnomad4 EAS exome

AF:

0.240

Gnomad4 SAS exome

AF:

0.735

Gnomad4 FIN exome

AF:

0.897

Gnomad4 NFE exome

AF:

0.823

Gnomad4 OTH exome

AF:

0.751

GnomAD4 genome

AF:

0.664

AC:

101047

AN:

152162

Hom.:

37103

Cov.:

AF XY:

0.666

AC XY:

49579

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.374

Gnomad4 AMR

AF:

0.628

Gnomad4 ASJ

AF:

0.821

Gnomad4 EAS

AF:

0.264

Gnomad4 SAS

AF:

0.722

Gnomad4 FIN

AF:

0.904

Gnomad4 NFE

AF:

0.826

Gnomad4 OTH

AF:

0.697

Alfa

AF:

0.795

Hom.:

79520

Bravo

AF:

0.625

Asia WGS

AF:

0.573

AC:

1989

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

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 -

Primary ciliary dyskinesia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Primary ciliary dyskinesia 21

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 30, 2021

- -

not provided

Benign:1

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

-1.0

CADD

Benign

0.0060

DANN

Benign

0.26

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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