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. The variant received -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
• Publications: 3 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130848.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCANP1	NM_130848.3	MANE Select	c.*983C>T		3_prime_UTR	Exon 1 of 1	NP_570900.1
	TIFAB	NM_001099221.2	MANE Select	c.*4063C>T		3_prime_UTR	Exon 2 of 2	NP_001092691.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCANP1	ENST00000503143.3	TSL:6 MANE Select	c.*983C>T		3_prime_UTR	Exon 1 of 1	ENSP00000421871.1
	TIFAB	ENST00000537858.2	TSL:1 MANE Select	c.*4063C>T		3_prime_UTR	Exon 2 of 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

African (AFR) AF: 0.417 AC: 5 AN: 12

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.200 AC: 2 AN: 10

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.375 AC: 3 AN: 8

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.242 AC: 58 AN: 240

Other (OTH) AF: 0.500 AC: 4 AN: 8

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

African (AFR) AF: 0.381 AC: 15784 AN: 41446

American (AMR) AF: 0.209 AC: 3198 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1761 AN: 5160

South Asian (SAS) AF: 0.313 AC: 1506 AN: 4816

European-Finnish (FIN) AF: 0.226 AC: 2385 AN: 10570

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17137 AN: 67968

Other (OTH) AF: 0.288 AC: 608 AN: 2110

Alfa AF: 0.261 Hom.: 2106

Bravo AF: 0.291

Asia WGS AF: 0.284 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.74
PhyloP100		0.29
Mutation Taster		=100/0	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: rs10061623; hg19: chr5-134781081;