Variant 10-101608897-T-C 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_015448.3(DPCD):c.467T>C(p.Leu156Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 1,612,594 control chromosomes in the GnomAD database, including 63,182 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.28 ( 6200 hom., cov: 31)

Exomes 𝑓: 0.27 ( 56982 hom. )

Consequence

DPCD
NM_015448.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.597

Variant links:

Genes affected

DPCD (HGNC:24542): (deleted in primary ciliary dyskinesia homolog (mouse)) This gene in mouse encodes a protein that may be involved in the generation and maintenance of ciliated cells. In mouse, expression of this gene increases during ciliated cell differentiation, and disruption of this gene has been linked to primary ciliary dyskinesia. [provided by RefSeq, Jul 2016]

DPCD 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 (MetaRNN=0.0027190149).

BP6

Variant 10-101608897-T-C is Benign according to our data. Variant chr10-101608897-T-C is described in ClinVar as [Benign]. Clinvar id is 1233427.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPCD	NM_015448.3 linkuse as main transcript	c.467T>C	p.Leu156Ser	missense_variant	5/6	ENST00000370151.9	NP_056263.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPCD	ENST00000370151.9 linkuse as main transcript	c.467T>C	p.Leu156Ser	missense_variant	5/6	1	NM_015448.3	ENSP00000359170	P1

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42650

AN:

151802

Hom.:

6195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.333

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.287

GnomAD3 exomes

AF:

0.249

AC:

62484

AN:

251266

Hom.:

8424

AF XY:

0.248

AC XY:

33617

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.306

Gnomad AMR exome

AF:

0.177

Gnomad ASJ exome

AF:

0.325

Gnomad EAS exome

AF:

0.153

Gnomad SAS exome

AF:

0.155

Gnomad FIN exome

AF:

0.249

Gnomad NFE exome

AF:

0.295

Gnomad OTH exome

AF:

0.269

GnomAD4 exome

AF:

0.275

AC:

401516

AN:

1460676

Hom.:

56982

Cov.:

AF XY:

0.272

AC XY:

197615

AN XY:

726682

show subpopulations

Gnomad4 AFR exome

AF:

0.306

Gnomad4 AMR exome

AF:

0.186

Gnomad4 ASJ exome

AF:

0.328

Gnomad4 EAS exome

AF:

0.133

Gnomad4 SAS exome

AF:

0.160

Gnomad4 FIN exome

AF:

0.252

Gnomad4 NFE exome

AF:

0.291

Gnomad4 OTH exome

AF:

0.279

GnomAD4 genome

AF:

0.281

AC:

42672

AN:

151918

Hom.:

6200

Cov.:

AF XY:

0.275

AC XY:

20457

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.253

Gnomad4 ASJ

AF:

0.333

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.152

Gnomad4 FIN

AF:

0.250

Gnomad4 NFE

AF:

0.295

Gnomad4 OTH

AF:

0.287

Alfa

AF:

0.290

Hom.:

16297

Bravo

AF:

0.282

TwinsUK

AF:

0.284

AC:

1052

ALSPAC

AF:

0.286

AC:

1101

ESP6500AA

AF:

0.307

AC:

1354

ESP6500EA

AF:

0.307

AC:

2639

ExAC

AF:

0.250

AC:

30337

Asia WGS

AF:

0.143

AC:

499

AN:

3478

EpiCase

AF:

0.302

EpiControl

AF:

0.304

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 23, 2020	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.048

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.14

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0067

T;T

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.017

LIST_S2

Benign

0.31

T;.

MetaRNN

Benign

0.0027

T;T

MetaSVM

Benign

-0.93

MutationTaster

Benign

1.0

P;P;P

PROVEAN

Benign

0.040

.;N

REVEL

Benign

0.027

Sift

Pathogenic

0.0

.;D

Vest4

0.063

ClinPred

0.0094

GERP RS

-0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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