12-103777677-C-T

Variant names:

• chr12-103777677-C-T
• rs3751204
• NM_001031701.3:c.*152G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NT5DC3	NM_001031701.3	c.*152G>A		3_prime_UTR_variant	Exon 14 of 14	ENST00000392876.8	NP_001026871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5DC3	ENST00000392876.8	c.*152G>A		3_prime_UTR_variant	Exon 14 of 14	1	NM_001031701.3	ENSP00000376615.3
NT5DC3	ENST00000447799.5	n.*152G>A		non_coding_transcript_exon_variant	Exon 3 of 5	2		ENSP00000413657.1
NT5DC3	ENST00000447799.5	n.*152G>A		3_prime_UTR_variant	Exon 3 of 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

African (AFR) AF: 0.242 AC: 4538 AN: 18780

American (AMR) AF: 0.316 AC: 6764 AN: 21392

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 5020 AN: 15592

East Asian (EAS) AF: 0.380 AC: 13150 AN: 34630

South Asian (SAS) AF: 0.456 AC: 23735 AN: 52016

European-Finnish (FIN) AF: 0.275 AC: 9418 AN: 34296

Middle Eastern (MID) AF: 0.346 AC: 877 AN: 2538

European-Non Finnish (NFE) AF: 0.273 AC: 145621 AN: 534050

Other (OTH) AF: 0.305 AC: 10966 AN: 35952

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

African (AFR) AF: 0.249 AC: 10325 AN: 41494

American (AMR) AF: 0.307 AC: 4688 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1135 AN: 3472

East Asian (EAS) AF: 0.426 AC: 2199 AN: 5168

South Asian (SAS) AF: 0.470 AC: 2269 AN: 4828

European-Finnish (FIN) AF: 0.287 AC: 3031 AN: 10560

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19253 AN: 67982

Other (OTH) AF: 0.294 AC: 620 AN: 2112

Alfa AF: 0.280 Hom.: 7968

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
PhyloP100		0.084
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: rs3751204; hg19: chr12-104171455;