Genetic Variant NUDT22:n.1556C>T (chr11-64227830-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000422364.2(NUDT22):n.1556C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

NUDT22
ENST00000422364.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.316

Publications

8 publications found

Variant links:

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]

NUDT22 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUDT22	NM_032344.4 link	c.579+164C>T		intron_variant	Intron 3 of 5	ENST00000279206.8	NP_115720.2	Q9BRQ3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUDT22	ENST00000279206.8 link	c.579+164C>T		intron_variant	Intron 3 of 5	1	NM_032344.4	ENSP00000279206.3		Q9BRQ3-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

460966

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

243862

African (AFR)

AF:

0.00

AC:

AN:

12582

American (AMR)

AF:

0.00

AC:

AN:

19140

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13844

East Asian (EAS)

AF:

0.00

AC:

AN:

31250

South Asian (SAS)

AF:

0.00

AC:

AN:

46734

European-Finnish (FIN)

AF:

0.00

AC:

AN:

35516

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2462

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

273154

Other (OTH)

AF:

0.00

AC:

AN:

26284

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.3

(source)

DANN

Benign

0.62

PhyloP100

-0.32

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over