22-42058350-G-A

Variant names:

• chr22-42058350-G-A
• rs5758566
• NM_000262.3:c.*1929C>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000262.3(NAGA):​c.*1929C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,864 control chromosomes in the GnomAD database, including 30,224 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.62 (30222 hom., cov: 30)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: NAGA NM_000262.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.585

Genes affected

NAGA (HGNC:7631): (alpha-N-acetylgalactosaminidase) NAGA encodes the lysosomal enzyme alpha-N-acetylgalactosaminidase, which cleaves alpha-N-acetylgalactosaminyl moieties from glycoconjugates. Mutations in NAGA have been identified as the cause of Schindler disease types I and II (type II also known as Kanzaki disease). [provided by RefSeq, Jul 2008]

WBP2NL (HGNC:28389): (WBP2 N-terminal like) WBP2NL is a sperm-specific WW domain-binding protein that promotes meiotic resumption and pronuclear development during oocyte fertilization (Wu et al., 2007 [PubMed 17289678]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 22-42058350-G-A is Benign according to our data. Variant chr22-42058350-G-A is described in ClinVar as [Benign]. Clinvar id is 341885.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAGA	NM_000262.3	c.*1929C>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000396398.8	NP_000253.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAGA	ENST00000396398	c.*1929C>T		3_prime_UTR_variant	Exon 9 of 9	1	NM_000262.3	ENSP00000379680.3
WBP2NL	ENST00000436265.5	n.*334G>A		non_coding_transcript_exon_variant	Exon 9 of 9	2		ENSP00000401002.1
WBP2NL	ENST00000436265.5	n.*334G>A		3_prime_UTR_variant	Exon 9 of 9	2		ENSP00000401002.1

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94885 AN: 151742 Hom.: 30220 Cov.: 30

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.630

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.625 AC: 94906 AN: 151860 Hom.: 30222 Cov.: 30 AF XY: 0.624 AC XY: 46292 AN XY: 74222

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.632

Alfa AF: 0.674 Hom.: 33021

Bravo AF: 0.627

Asia WGS AF: 0.718 AC: 2499 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Alpha-N-acetylgalactosaminidase deficiency type 2 Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Alpha-N-acetylgalactosaminidase deficiency type 1 Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5758566; hg19: chr22-42454354;