rs7744809

Variant names:

• chr6-116231903-G-A
• rs7744809
• NM_152729.3:c.803-5063G>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.803-5063G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,122 control chromosomes in the GnomAD database, including 9,297 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 0.32 (9297 hom., cov: 33)
• Consequence: NT5DC1 NM_152729.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

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.803-5063G>A		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.803-5063G>A		intron	N/A	ENSP00000326858.3	Q5TFE4-1
	NT5DC1	ENST00000880964.1		c.803-5063G>A		intron	N/A	ENSP00000551023.1
	NT5DC1	ENST00000880963.1		c.779-5063G>A		intron	N/A	ENSP00000551022.1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48741 AN: 152002 Hom.: 9290 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.321 AC: 48763 AN: 152122 Hom.: 9297 Cov.: 33 AF XY: 0.329 AC XY: 24430 AN XY: 74354

African (AFR) AF: 0.121 AC: 5014 AN: 41504

American (AMR) AF: 0.375 AC: 5735 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3470

East Asian (EAS) AF: 0.660 AC: 3424 AN: 5188

South Asian (SAS) AF: 0.542 AC: 2611 AN: 4816

European-Finnish (FIN) AF: 0.422 AC: 4453 AN: 10556

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25171 AN: 67988

Other (OTH) AF: 0.335 AC: 707 AN: 2112

Alfa AF: 0.333 Hom.: 1191

Bravo AF: 0.308

Asia WGS AF: 0.490 AC: 1704 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.48
PhyloP100		-0.15
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: rs7744809; hg19: chr6-116553066; COSMIC: COSV60307252;