chr6-34287699-T-C

Position:

• chr6-34287699-T-C

Variant summary

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

The NM_006703.4(NUDT3):​c.*1054A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,166 control chromosomes in the GnomAD database, including 9,925 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 0.33 (9924 hom., cov: 32)
  • Exomes 𝑓: 0.22 (1 hom.)
• Consequence: NUDT3 NM_006703.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUDT3	NM_006703.4	c.*1054A>G		3_prime_UTR_variant	5/5	ENST00000607016.2	NP_006694.1
RPS10-NUDT3	NM_001202470.3	c.*1054A>G		3_prime_UTR_variant	9/9		NP_001189399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUDT3	ENST00000607016.2	c.*1054A>G		3_prime_UTR_variant	5/5	1	NM_006703.4	ENSP00000476119.1
RPS10-NUDT3	ENST00000639725	c.*1054A>G		3_prime_UTR_variant	9/9	5		ENSP00000492441.1
RPS10-NUDT3	ENST00000639877	c.*1054A>G		3_prime_UTR_variant	9/9	5		ENSP00000491891.1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50220 AN: 151994 Hom.: 9877 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.352

GnomAD4 exome AF: 0.222 AC: 12 AN: 54 Hom.: 1 Cov.: 0 AF XY: 0.208 AC XY: 10 AN XY: 48

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.278

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.331 AC: 50320 AN: 152112 Hom.: 9924 Cov.: 32 AF XY: 0.333 AC XY: 24785 AN XY: 74362

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.351

Alfa AF: 0.290 Hom.: 1586

Bravo AF: 0.356

Asia WGS AF: 0.447 AC: 1554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.37
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs206942; hg19: chr6-34255476;