Variant chr2-26401975-C-T 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.-15C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 1,590,130 control chromosomes in the GnomAD database, including 746 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.021 ( 51 hom., cov: 32)

Exomes 𝑓: 0.028 ( 695 hom. )

Consequence

DRC1
NM_145038.5 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.865

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=-0.8).

BP6

Variant 2-26401975-C-T is Benign according to our data. Variant chr2-26401975-C-T is described in ClinVar as [Benign]. Clinvar id is 1275914.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DRC1	NM_145038.5 linkuse as main transcript	c.-15C>T		5_prime_UTR_variant	1/17	ENST00000288710.7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
DRC1	ENST00000288710.7 linkuse as main transcript	c.-15C>T	5_prime_UTR_variant	1/17	2	NM_145038.5	P1
DRC1	ENST00000421869.5 linkuse as main transcript	c.-15C>T	5_prime_UTR_variant, NMD_transcript_variant	1/8	1
DRC1	ENST00000649059.1 linkuse as main transcript		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0206

AC:

3141

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00635

Gnomad AMI

AF:

0.00659

Gnomad AMR

AF:

0.0160

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.0638

Gnomad SAS

AF:

0.0147

Gnomad FIN

AF:

0.0180

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0286

Gnomad OTH

AF:

0.0220

GnomAD3 exomes

AF:

0.0233

AC:

4854

AN:

208666

Hom.:

AF XY:

0.0237

AC XY:

2677

AN XY:

113064

show subpopulations

Gnomad AFR exome

AF:

0.00507

Gnomad AMR exome

AF:

0.0113

Gnomad ASJ exome

AF:

0.0147

Gnomad EAS exome

AF:

0.0622

Gnomad SAS exome

AF:

0.0121

Gnomad FIN exome

AF:

0.0179

Gnomad NFE exome

AF:

0.0281

Gnomad OTH exome

AF:

0.0274

GnomAD4 exome

AF:

0.0277

AC:

39841

AN:

1437854

Hom.:

695

Cov.:

AF XY:

0.0274

AC XY:

19519

AN XY:

713018

show subpopulations

Gnomad4 AFR exome

AF:

0.00457

Gnomad4 AMR exome

AF:

0.0119

Gnomad4 ASJ exome

AF:

0.0127

Gnomad4 EAS exome

AF:

0.0849

Gnomad4 SAS exome

AF:

0.0134

Gnomad4 FIN exome

AF:

0.0200

Gnomad4 NFE exome

AF:

0.0289

Gnomad4 OTH exome

AF:

0.0259

GnomAD4 genome

AF:

0.0206

AC:

3138

AN:

152276

Hom.:

Cov.:

AF XY:

0.0200

AC XY:

1489

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.00633

Gnomad4 AMR

AF:

0.0159

Gnomad4 ASJ

AF:

0.0112

Gnomad4 EAS

AF:

0.0639

Gnomad4 SAS

AF:

0.0145

Gnomad4 FIN

AF:

0.0180

Gnomad4 NFE

AF:

0.0286

Gnomad4 OTH

AF:

0.0213

Alfa

AF:

0.0223

Hom.:

Bravo

AF:

0.0200

Asia WGS

AF:

0.0480

AC:

166

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.0

DANN

Benign

0.64

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