16-77733594-A-G

Variant names:

• chr16-77733594-A-G
• rs16946398
• NM_001105663.3:c.190-2234A>G

Variant summary

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

The NM_001105663.3(NUDT7):​c.190-2234A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,284 control chromosomes in the GnomAD database, including 919 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 0.10 (919 hom., cov: 33)
• Consequence: NUDT7 NM_001105663.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 5 publications found

Genes affected

NUDT7 (HGNC:8054): (nudix hydrolase 7) The protein encoded by this gene is a member of the Nudix hydrolase family. Nudix hydrolases eliminate potentially toxic nucleotide metabolites from the cell and regulate the concentrations and availability of many different nucleotide substrates, cofactors, and signaling molecules. Alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUDT7	NM_001105663.3	c.190-2234A>G		intron_variant	Intron 2 of 3	ENST00000268533.9	NP_001099133.1
NUDT7	NM_001243660.2	c.190-1800A>G		intron_variant	Intron 2 of 3		NP_001230589.1
NUDT7	NM_001243661.2	c.190-7988A>G		intron_variant	Intron 2 of 2		NP_001230590.1
NUDT7	NM_001243657.2	c.190-2234A>G		intron_variant	Intron 2 of 4		NP_001230586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUDT7	ENST00000268533.9	c.190-2234A>G		intron_variant	Intron 2 of 3	1	NM_001105663.3	ENSP00000268533.5

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15603 AN: 152166 Hom.: 913 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.103 AC: 15628 AN: 152284 Hom.: 919 Cov.: 33 AF XY: 0.102 AC XY: 7572 AN XY: 74478

African (AFR) AF: 0.161 AC: 6673 AN: 41542

American (AMR) AF: 0.122 AC: 1866 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3470

East Asian (EAS) AF: 0.146 AC: 755 AN: 5180

South Asian (SAS) AF: 0.0458 AC: 221 AN: 4826

European-Finnish (FIN) AF: 0.0478 AC: 508 AN: 10618

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0727 AC: 4946 AN: 68024

Other (OTH) AF: 0.106 AC: 225 AN: 2116

Alfa AF: 0.0822 Hom.: 1870

Bravo AF: 0.110

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.75
PhyloP100		0.14
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: rs16946398; hg19: chr16-77767491;