chr6-116109640-G-A

Variant names:

• chr6-116109640-G-A
• rs568725
• NM_152729.3:c.257+1205G>A

Variant summary

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

The NM_152729.3(NT5DC1):​c.257+1205G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,040 control chromosomes in the GnomAD database, including 27,996 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 0.60 (27996 hom., cov: 32)
• Consequence: NT5DC1 NM_152729.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NT5DC1	NM_152729.3	c.257+1205G>A		intron_variant	Intron 3 of 11	ENST00000319550.9	NP_689942.2
NT5DC1	XM_006715378.4	c.257+1205G>A		intron_variant	Intron 3 of 9		XP_006715441.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5DC1	ENST00000319550.9	c.257+1205G>A		intron_variant	Intron 3 of 11	1	NM_152729.3	ENSP00000326858.3
NT5DC1	ENST00000419791.3	c.257+1205G>A		intron_variant	Intron 3 of 6	3		ENSP00000393578.1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91605 AN: 151922 Hom.: 27972 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.603 AC: 91667 AN: 152040 Hom.: 27996 Cov.: 32 AF XY: 0.610 AC XY: 45321 AN XY: 74310

African (AFR) AF: 0.513 AC: 21250 AN: 41440

American (AMR) AF: 0.681 AC: 10404 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3472

East Asian (EAS) AF: 0.780 AC: 4042 AN: 5182

South Asian (SAS) AF: 0.790 AC: 3804 AN: 4818

European-Finnish (FIN) AF: 0.644 AC: 6814 AN: 10576

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41106 AN: 67954

Other (OTH) AF: 0.610 AC: 1290 AN: 2116

Alfa AF: 0.599 Hom.: 3571

Bravo AF: 0.602

Asia WGS AF: 0.723 AC: 2517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.031
DANN	Benign	0.35
PhyloP100		-2.2
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: rs568725; hg19: chr6-116430803; COSMIC: COSV60307193; COSMIC: COSV60307193;