12-103777677-C-T

Position:

• chr12-103777677-C-T

Variant summary

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

The NM_001031701.3(NT5DC3):​c.*152G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 901,358 control chromosomes in the GnomAD database, including 40,339 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 (6544 hom., cov: 33)
  • Exomes 𝑓: 0.29 (33795 hom.)
• Consequence: NT5DC3 NM_001031701.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

Genes affected

NT5DC3 (HGNC:30826): (5'-nucleotidase domain containing 3) Predicted to enable 5'-nucleotidase activity. Predicted to be involved in dephosphorylation. Part of receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

NT5DC3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5DC3	NM_001031701.3	c.*152G>A		3_prime_UTR_variant	14/14	ENST00000392876.8	NP_001026871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5DC3	ENST00000392876	c.*152G>A		3_prime_UTR_variant	14/14	1	NM_001031701.3	ENSP00000376615.3
NT5DC3	ENST00000447799.5	n.*152G>A		non_coding_transcript_exon_variant	3/5	2		ENSP00000413657.1
NT5DC3	ENST00000447799.5	n.*152G>A		3_prime_UTR_variant	3/5	2		ENSP00000413657.1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43900 AN: 151994 Hom.: 6537 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.291

GnomAD4 exome AF: 0.294 AC: 220089 AN: 749246 Hom.: 33795 Cov.: 10 AF XY: 0.300 AC XY: 114570 AN XY: 381448

Gnomad4 AFR exome AF: 0.242

Gnomad4 AMR exome AF: 0.316

Gnomad4 ASJ exome AF: 0.322

Gnomad4 EAS exome AF: 0.380

Gnomad4 SAS exome AF: 0.456

Gnomad4 FIN exome AF: 0.275

Gnomad4 NFE exome AF: 0.273

Gnomad4 OTH exome AF: 0.305

GnomAD4 genome AF: 0.289 AC: 43914 AN: 152112 Hom.: 6544 Cov.: 33 AF XY: 0.294 AC XY: 21846 AN XY: 74374

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.294

Alfa AF: 0.280 Hom.: 6136

Bravo AF: 0.284

Asia WGS AF: 0.455 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.40

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: rs3751204; hg19: chr12-104171455;