rs10061623

Variant names:

• chr5-135445391-G-A
• rs10061623
• NM_130848.3:c.*983C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-135445391-G-A
• chr5-135445391-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_130848.3(DCANP1):​c.*983C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,324 control chromosomes in the GnomAD database, including 6,635 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 0.29 (6625 hom., cov: 32)
  • Exomes 𝑓: 0.25 (10 hom.)
• Consequence: DCANP1 NM_130848.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCANP1	NM_130848.3	c.*983C>T		3_prime_UTR_variant	Exon 1 of 1	ENST00000503143.3	NP_570900.1
TIFAB	NM_001099221.2	c.*4063C>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	c.*983C>T		3_prime_UTR_variant	Exon 1 of 1		NM_130848.3	ENSP00000421871.1
TIFAB	ENST00000537858	c.*4063C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_001099221.2	ENSP00000440509.1

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43409 AN: 151924 Hom.: 6623 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.291

GnomAD4 exome AF: 0.254 AC: 72 AN: 284 Hom.: 10 Cov.: 0 AF XY: 0.243 AC XY: 53 AN XY: 218

Gnomad4 AFR exome AF: 0.417

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.200

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.242

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.286 AC: 43427 AN: 152040 Hom.: 6625 Cov.: 32 AF XY: 0.286 AC XY: 21274 AN XY: 74308

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.288

Alfa AF: 0.255 Hom.: 1602

Bravo AF: 0.291

Asia WGS AF: 0.284 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs10061623; hg19: chr5-134781081;