rs1204830

Positions:

• chr6-116249325-A-G
• chr6-116249325-A-T

Variant summary

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

The NM_152729.3(NT5DC1):​c.*5301A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,142 control chromosomes in the GnomAD database, including 4,474 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 0.23 (4474 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: NT5DC1 NM_152729.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

NT5DC1 (HGNC:21556): (5'-nucleotidase domain containing 1) While the exact function of the protein encoded by this gene is not known, it belongs to the 5'(3')-deoxyribonucleotidase family. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5DC1	NM_152729.3	c.*5301A>G		3_prime_UTR_variant	12/12	ENST00000319550.9	NP_689942.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5DC1	ENST00000319550.9	c.*5301A>G		3_prime_UTR_variant	12/12	1	NM_152729.3	ENSP00000326858	P1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35587 AN: 152024 Hom.: 4462 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.228

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.234 AC: 35639 AN: 152142 Hom.: 4474 Cov.: 33 AF XY: 0.237 AC XY: 17637 AN XY: 74380

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.232

Alfa AF: 0.188 Hom.: 2300

Bravo AF: 0.240

Asia WGS AF: 0.346 AC: 1199 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.4
DANN	Benign	0.85

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: rs1204830; hg19: chr6-116570488;