12-103799046-C-G

Variant names:

• chr12-103799046-C-G
• rs4964805
• NM_001031701.3:c.525-369G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001031701.3(NT5DC3):​c.525-369G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,036 control chromosomes in the GnomAD database, including 6,140 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 0.27 (6140 hom., cov: 32)
• Consequence: NT5DC3 NM_001031701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 22 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NT5DC3	NM_001031701.3	c.525-369G>C		intron_variant	Intron 4 of 13	ENST00000392876.8	NP_001026871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5DC3	ENST00000392876.8	c.525-369G>C		intron_variant	Intron 4 of 13	1	NM_001031701.3	ENSP00000376615.3
NT5DC3	ENST00000465502.1	n.323-369G>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41445 AN: 151918 Hom.: 6134 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.251

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.273 AC: 41469 AN: 152036 Hom.: 6140 Cov.: 32 AF XY: 0.283 AC XY: 21019 AN XY: 74318

African (AFR) AF: 0.268 AC: 11082 AN: 41422

American (AMR) AF: 0.275 AC: 4205 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3470

East Asian (EAS) AF: 0.588 AC: 3042 AN: 5176

South Asian (SAS) AF: 0.530 AC: 2560 AN: 4830

European-Finnish (FIN) AF: 0.301 AC: 3180 AN: 10572

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15794 AN: 67968

Other (OTH) AF: 0.255 AC: 539 AN: 2112

Alfa AF: 0.232 Hom.: 527

Bravo AF: 0.266

Asia WGS AF: 0.542 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		-0.28
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: rs4964805; hg19: chr12-104192824;