5-135446760-T-A

Variant names:

• chr5-135446760-T-A
• rs12520799
• NM_130848.3:c.349A>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_130848.3(DCANP1):​c.349A>T​(p.Arg117*) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 44 publications found

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]

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]

ENSG00000249639 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DCANP1	NM_130848.3	c.349A>T	p.Arg117*	stop_gained	Exon 1 of 1	ENST00000503143.3	NP_570900.1
TIFAB	NM_001099221.2	c.*2694A>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000537858.2	NP_001092691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCANP1	ENST00000503143.3	c.349A>T	p.Arg117*	stop_gained	Exon 1 of 1	6	NM_130848.3	ENSP00000421871.1
TIFAB	ENST00000537858.2	c.*2694A>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_001099221.2	ENSP00000440509.1
ENSG00000249639	ENST00000732724.1	n.118+617T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88896 AN: 151924 Hom.: 28592 Cov.: 32

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

GnomAD2 exomes AF: 0.510 AC: 128099 AN: 251084 AF XY: 0.503

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 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.: 66 AF XY: 0.482 AC XY: 350160 AN XY: 726944

African (AFR) AF: 0.882 AC: 29511 AN: 33460

American (AMR) AF: 0.530 AC: 23720 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 12160 AN: 26136

East Asian (EAS) AF: 0.525 AC: 20825 AN: 39698

South Asian (SAS) AF: 0.519 AC: 44782 AN: 86250

European-Finnish (FIN) AF: 0.389 AC: 20749 AN: 53400

Middle Eastern (MID) AF: 0.548 AC: 3160 AN: 5766

European-Non Finnish (NFE) AF: 0.467 AC: 518896 AN: 1111512

Other (OTH) AF: 0.513 AC: 30983 AN: 60360

GnomAD4 genome AF: 0.585 AC: 89011 AN: 152042 Hom.: 28651 Cov.: 32 AF XY: 0.583 AC XY: 43303 AN XY: 74296

African (AFR) AF: 0.871 AC: 36148 AN: 41486

American (AMR) AF: 0.554 AC: 8470 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1646 AN: 3470

East Asian (EAS) AF: 0.574 AC: 2949 AN: 5140

South Asian (SAS) AF: 0.521 AC: 2512 AN: 4820

European-Finnish (FIN) AF: 0.393 AC: 4152 AN: 10576

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.461 AC: 31354 AN: 67950

Other (OTH) AF: 0.594 AC: 1253 AN: 2110

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	T
BayesDel_noAF	Benign	-0.11
CADD	Pathogenic	34
DANN	Benign	0.95
Eigen	Benign	-0.38
Eigen_PC	Benign	-0.86
FATHMM_MKL	Benign	0.00039	N
PhyloP100		-0.21
Vest4		0.051
GERP RS		-5.9
Mutation Taster		=196/4	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12520799; hg19: chr5-134782450; COSMIC: COSV72345715; COSMIC: COSV72345715;