11-64227830-C-G

Variant names:

• chr11-64227830-C-G
• rs2429455
• ENST00000422364.2:n.1556C>G

Variant summary

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

The ENST00000422364.2(NUDT22):​n.1556C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 612,428 control chromosomes in the GnomAD database, including 143,456 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 0.67 (34579 hom., cov: 31)
  • Exomes 𝑓: 0.69 (108877 hom.)
• Consequence: NUDT22 ENST00000422364.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 8 publications found

Genes affected

NUDT22 (HGNC:28189): (nudix hydrolase 22) Enables UDP-sugar diphosphatase activity and metal ion binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUDT22	NM_032344.4	c.579+164C>G		intron_variant	Intron 3 of 5	ENST00000279206.8	NP_115720.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUDT22	ENST00000279206.8	c.579+164C>G		intron_variant	Intron 3 of 5	1	NM_032344.4	ENSP00000279206.3

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102269 AN: 151882 Hom.: 34565 Cov.: 31

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.665

GnomAD4 exome AF: 0.686 AC: 315654 AN: 460428 Hom.: 108877 Cov.: 4 AF XY: 0.694 AC XY: 169094 AN XY: 243608

African (AFR) AF: 0.684 AC: 8591 AN: 12554

American (AMR) AF: 0.594 AC: 11351 AN: 19100

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 10592 AN: 13828

East Asian (EAS) AF: 0.682 AC: 21276 AN: 31206

South Asian (SAS) AF: 0.825 AC: 38511 AN: 46686

European-Finnish (FIN) AF: 0.696 AC: 24681 AN: 35458

Middle Eastern (MID) AF: 0.758 AC: 1864 AN: 2460

European-Non Finnish (NFE) AF: 0.663 AC: 180997 AN: 272872

Other (OTH) AF: 0.677 AC: 17791 AN: 26264

GnomAD4 genome AF: 0.673 AC: 102328 AN: 152000 Hom.: 34579 Cov.: 31 AF XY: 0.676 AC XY: 50259 AN XY: 74312

African (AFR) AF: 0.682 AC: 28282 AN: 41472

American (AMR) AF: 0.606 AC: 9262 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2650 AN: 3470

East Asian (EAS) AF: 0.715 AC: 3687 AN: 5160

South Asian (SAS) AF: 0.831 AC: 4006 AN: 4818

European-Finnish (FIN) AF: 0.708 AC: 7473 AN: 10560

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44697 AN: 67922

Other (OTH) AF: 0.662 AC: 1394 AN: 2106

Alfa AF: 0.567 Hom.: 1605

Bravo AF: 0.663

Asia WGS AF: 0.746 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.99
DANN	Benign	0.59
PhyloP100		-0.32
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: rs2429455; hg19: chr11-63995302;