6-116168387-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.529+50442A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,796 control chromosomes in the GnomAD database, including 3,367 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 0.19 (3367 hom., cov: 32)
• Consequence: NT5DC1 NM_152729.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

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]

COL10A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5DC1	NM_152729.3	c.529+50442A>G		intron_variant		ENST00000319550.9
NT5DC1	XM_006715378.4	c.529+50442A>G		intron_variant
COL10A1	XM_011535432.4	c.-15-42880T>C		intron_variant
COL10A1	XM_011535433.4	c.-16+40876T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5DC1	ENST00000319550.9	c.529+50442A>G		intron_variant		1	NM_152729.3	P1
NT5DC1	ENST00000460749.1	c.27+50442A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28880 AN: 151678 Hom.: 3369 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.0622

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.190 AC: 28873 AN: 151796 Hom.: 3367 Cov.: 32 AF XY: 0.183 AC XY: 13592 AN XY: 74202

Gnomad4 AFR AF: 0.0873

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.0627

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.221

Alfa AF: 0.208 Hom.: 698

Bravo AF: 0.189

Asia WGS AF: 0.0400 AC: 141 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.7
Dann	Benign	0.69
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs12196141; hg19: chr6-116489550;