Variant chr5-135446760-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_130848.3(DCANP1):c.349A>T(p.Arg117Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 1,613,342 control chromosomes in the GnomAD database, including 202,748 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.59 ( 28651 hom., cov: 32)

Exomes 𝑓: 0.48 ( 174097 hom. )

Consequence

DCANP1
NM_130848.3 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.208

Variant links:

Genes affected

DCANP1 (HGNC:24459): (dendritic cell associated nuclear protein 1) This intronless gene is specifically expressed in dendritic cells (DCs), which are potent antigen-presenting cells involved in activating naive T cells to initiate antigen-specific immune response. The encoded protein is localized mainly in the perinucleus. One of the alleles (A/T) of this gene, that causes premature translation termination at aa 117, has been associated with an increased prevalence of major depression in humans. [provided by RefSeq, Jul 2008]

DCANP1 links:

TIFAB (HGNC:34024): (TIFA inhibitor) Involved in several processes, including animal organ morphogenesis; cranial nerve development; and hard palate morphogenesis. [provided by Alliance of Genome Resources, Apr 2022]

TIFAB links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCANP1	NM_130848.3 linkuse as main transcript	c.349A>T	p.Arg117Ter	stop_gained	1/1	ENST00000503143.3	NP_570900.1
TIFAB	NM_001099221.2 linkuse as main transcript	c.*2694A>T		3_prime_UTR_variant	2/2	ENST00000537858.2	NP_001092691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCANP1	ENST00000503143.3 linkuse as main transcript	c.349A>T	p.Arg117Ter	stop_gained	1/1		NM_130848.3	ENSP00000421871	P1
TIFAB	ENST00000537858.2 linkuse as main transcript	c.*2694A>T		3_prime_UTR_variant	2/2	1	NM_001099221.2	ENSP00000440509	P1

Frequencies

GnomAD3 genomes

AF:

0.585

AC:

88896

AN:

151924

Hom.:

28592

Cov.:

show subpopulations

Gnomad AFR

AF:

0.871

Gnomad AMI

AF:

0.413

Gnomad AMR

AF:

0.554

Gnomad ASJ

AF:

0.474

Gnomad EAS

AF:

0.573

Gnomad SAS

AF:

0.521

Gnomad FIN

AF:

0.393

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.461

Gnomad OTH

AF:

0.592

GnomAD3 exomes

AF:

0.510

AC:

128099

AN:

251084

Hom.:

34131

AF XY:

0.503

AC XY:

68322

AN XY:

135702

show subpopulations

Gnomad AFR exome

AF:

0.881

Gnomad AMR exome

AF:

0.524

Gnomad ASJ exome

AF:

0.471

Gnomad EAS exome

AF:

0.579

Gnomad SAS exome

AF:

0.519

Gnomad FIN exome

AF:

0.384

Gnomad NFE exome

AF:

0.467

Gnomad OTH exome

AF:

0.513

GnomAD4 exome

AF:

0.482

AC:

704786

AN:

1461300

Hom.:

174097

Cov.:

AF XY:

0.482

AC XY:

350160

AN XY:

726944

show subpopulations

Gnomad4 AFR exome

AF:

0.882

Gnomad4 AMR exome

AF:

0.530

Gnomad4 ASJ exome

AF:

0.465

Gnomad4 EAS exome

AF:

0.525

Gnomad4 SAS exome

AF:

0.519

Gnomad4 FIN exome

AF:

0.389

Gnomad4 NFE exome

AF:

0.467

Gnomad4 OTH exome

AF:

0.513

GnomAD4 genome

AF:

0.585

AC:

89011

AN:

152042

Hom.:

28651

Cov.:

AF XY:

0.583

AC XY:

43303

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.871

Gnomad4 AMR

AF:

0.554

Gnomad4 ASJ

AF:

0.474

Gnomad4 EAS

AF:

0.574

Gnomad4 SAS

AF:

0.521

Gnomad4 FIN

AF:

0.393

Gnomad4 NFE

AF:

0.461

Gnomad4 OTH

AF:

0.594

Alfa

AF:

0.482

Hom.:

14077

Bravo

AF:

0.614

TwinsUK

AF:

0.467

AC:

1731

ALSPAC

AF:

0.471

AC:

1815

ESP6500AA

AF:

0.862

AC:

3799

ESP6500EA

AF:

0.463

AC:

3985

ExAC

AF:

0.517

AC:

62832

Asia WGS

AF:

0.559

AC:

1945

AN:

3478

EpiCase

AF:

0.483

EpiControl

AF:

0.482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.11

CADD

Pathogenic

DANN

Benign

0.95

Eigen

Benign

-0.38

Eigen_PC

Benign

-0.86

FATHMM_MKL

Benign

0.00039

MutationTaster

Benign

1.0

P;P

Vest4

0.051

GERP RS

-5.9

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over