rs206936

Variant names:

• chr6-34335092-A-G
• rs206936
• NM_006703.4:c.210+6770T>C

Variant summary

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

The NM_006703.4(NUDT3):​c.210+6770T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,050 control chromosomes in the GnomAD database, including 10,459 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 0.34 (10459 hom., cov: 31)
• Consequence: NUDT3 NM_006703.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.706
• Publications: 153 publications found

Genes affected

NUDT3 (HGNC:8050): (nudix hydrolase 3) NUDT3 belongs to the MutT, or Nudix, protein family. Nudix proteins act as homeostatic checkpoints at important stages in nucleoside phosphate metabolic pathways, guarding against elevated levels of potentially dangerous intermediates, like 8-oxo-dGTP, which promotes AT-to-CG transversions (Safrany et al., 1998 [PubMed 9822604]).[supplied by OMIM, Feb 2011]

RPS10-NUDT3 (HGNC:49181): (RPS10-NUDT3 readthrough) This locus represents naturally occurring read-through transcription between the neighboring RPS10 (ribosomal protein S10) and NUDT3 (nudix (nucleoside diphosphate linked moiety X)-type motif 3) genes on chromosome 6. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Feb 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUDT3	NM_006703.4	c.210+6770T>C		intron_variant	Intron 2 of 4	ENST00000607016.2	NP_006694.1
RPS10-NUDT3	NM_001202470.3	c.567+6770T>C		intron_variant	Intron 6 of 8		NP_001189399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUDT3	ENST00000607016.2	c.210+6770T>C		intron_variant	Intron 2 of 4	1	NM_006703.4	ENSP00000476119.1
RPS10-NUDT3	ENST00000639725.1	c.567+6770T>C		intron_variant	Intron 6 of 8	5		ENSP00000492441.1
RPS10-NUDT3	ENST00000639877.1	c.567+6770T>C		intron_variant	Intron 6 of 8	5		ENSP00000491891.1
RPS10-NUDT3	ENST00000605528.2	c.382-39407T>C		intron_variant	Intron 4 of 6	5		ENSP00000475027.2

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50981 AN: 151932 Hom.: 10412 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.336 AC: 51081 AN: 152050 Hom.: 10459 Cov.: 31 AF XY: 0.338 AC XY: 25130 AN XY: 74328

African (AFR) AF: 0.542 AC: 22443 AN: 41424

American (AMR) AF: 0.405 AC: 6198 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 883 AN: 3468

East Asian (EAS) AF: 0.486 AC: 2516 AN: 5172

South Asian (SAS) AF: 0.370 AC: 1783 AN: 4816

European-Finnish (FIN) AF: 0.224 AC: 2370 AN: 10582

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.204 AC: 13852 AN: 67988

Other (OTH) AF: 0.343 AC: 726 AN: 2114

Alfa AF: 0.251 Hom.: 23627

Bravo AF: 0.362

Asia WGS AF: 0.465 AC: 1615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.78
PhyloP100		0.71
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: rs206936; hg19: chr6-34302869;