6-116102081-T-G

Variant names:

• chr6-116102081-T-G
• rs509859
• NM_152729.3:c.93+1058T>G

Variant summary

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

The NM_152729.3(NT5DC1):​c.93+1058T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,148 control chromosomes in the GnomAD database, including 30,672 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 0.63 (30672 hom., cov: 33)
• Consequence: NT5DC1 NM_152729.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NT5DC1	NM_152729.3	c.93+1058T>G		intron_variant	Intron 1 of 11	ENST00000319550.9	NP_689942.2
NT5DC1	XM_006715378.4	c.93+1058T>G		intron_variant	Intron 1 of 9		XP_006715441.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5DC1	ENST00000319550.9	c.93+1058T>G		intron_variant	Intron 1 of 11	1	NM_152729.3	ENSP00000326858.3
NT5DC1	ENST00000419791.3	c.93+1058T>G		intron_variant	Intron 1 of 6	3		ENSP00000393578.1

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95638 AN: 152030 Hom.: 30655 Cov.: 33

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.629 AC: 95690 AN: 152148 Hom.: 30672 Cov.: 33 AF XY: 0.638 AC XY: 47480 AN XY: 74384

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.622

Alfa AF: 0.636 Hom.: 5424

Bravo AF: 0.629

Asia WGS AF: 0.833 AC: 2896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.8
DANN	Benign	0.87

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: rs509859; hg19: chr6-116423244;