6-116113881-C-T

Variant names:

• chr6-116113881-C-T
• rs1931898
• NM_152729.3:c.365-1810C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_152729.3(NT5DC1):​c.365-1810C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0123 in 152,256 control chromosomes in the GnomAD database, including 18 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 0.012 (18 hom., cov: 32)
• Consequence: NT5DC1 NM_152729.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0123 (1880/152256) while in subpopulation NFE AF = 0.0181 (1233/68016). AF 95% confidence interval is 0.0173. There are 18 homozygotes in GnomAd4. There are 918 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 18 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152729.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5DC1	NM_152729.3	MANE Select	c.365-1810C>T		intron	N/A	NP_689942.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5DC1	ENST00000319550.9	TSL:1 MANE Select	c.365-1810C>T		intron	N/A	ENSP00000326858.3	Q5TFE4-1
	NT5DC1	ENST00000880964.1		c.365-1810C>T		intron	N/A	ENSP00000551023.1
	NT5DC1	ENST00000880963.1		c.365-1810C>T		intron	N/A	ENSP00000551022.1

Frequencies

GnomAD3 genomes AF: 0.0124 AC: 1880 AN: 152138 Hom.: 18 Cov.: 32

Gnomad AFR AF: 0.00309

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.00910

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.00860

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

GnomAD4 genome AF: 0.0123 AC: 1880 AN: 152256 Hom.: 18 Cov.: 32 AF XY: 0.0123 AC XY: 918 AN XY: 74450

African (AFR) AF: 0.00308 AC: 128 AN: 41550

American (AMR) AF: 0.00902 AC: 138 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4824

European-Finnish (FIN) AF: 0.0266 AC: 282 AN: 10600

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0181 AC: 1233 AN: 68016

Other (OTH) AF: 0.00851 AC: 18 AN: 2116

Alfa AF: 0.00941 Hom.: 1

Bravo AF: 0.0111

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.62
PhyloP100		-0.89
Mutation Taster		=100/0	polymorphism

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: rs1931898; hg19: chr6-116435044;