rs1204798

chr6-116222684-A-G

Variant summary

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

The NM_152729.3(NT5DC1):c.705-350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,048 control chromosomes in the GnomAD database, including 16,443 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 0.41 (16443 hom., cov: 32)
• Consequence: NT5DC1 NM_152729.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5DC1	NM_152729.3	c.705-350A>G		intron_variant		ENST00000319550.9
NT5DC1	XM_006715378.4	c.705-350A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5DC1	ENST00000319550.9	c.705-350A>G		intron_variant		1	NM_152729.3	P1
NT5DC1	ENST00000460749.1	c.179-350A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62857 AN: 151930 Hom.: 16403 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.414 AC: 62947 AN: 152048 Hom.: 16443 Cov.: 32 AF XY: 0.416 AC XY: 30888 AN XY: 74300

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.374

Alfa AF: 0.308 Hom.: 3992

Bravo AF: 0.430

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.0
Dann	Benign	0.59

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: rs1204798; hg19: chr6-116543847;