Genetic Variant SNU13:c.*661A>G (chr22-41674272-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001003796.2(SNU13):c.*661A>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 0.831 in 152,796 control chromosomes in the GnomAD database, including 53,768 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 0.83 ( 53592 hom., cov: 32)

Exomes 𝑓: 0.67 ( 176 hom. )

Consequence

SNU13
NM_001003796.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.41

Publications

17 publications found

Variant links:

Genes affected

SNU13 (HGNC:7819): (small nuclear ribonucleoprotein 13) Originally named because of its sequence similarity to the Saccharomyces cerevisiae NHP2 (non-histone protein 2), this protein appears to be a highly conserved nuclear protein that is a component of the [U4/U6.U5] tri-snRNP. It binds to the 5' stem-loop of U4 snRNA. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

SNU13 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001003796.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNU13	NM_001003796.2	MANE Select	c.*661A>G		3_prime_UTR	Exon 3 of 3	NP_001003796.1
	SNU13	NM_005008.4		c.*661A>G		3_prime_UTR	Exon 4 of 4	NP_004999.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNU13	ENST00000401959.6	TSL:2 MANE Select	c.*661A>G		3_prime_UTR	Exon 3 of 3	ENSP00000383949.1
	SNU13	ENST00000648161.1		n.1002A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.831

AC:

126394

AN:

152014

Hom.:

53531

Cov.:

show subpopulations

Gnomad AFR

AF:

0.955

Gnomad AMI

AF:

0.701

Gnomad AMR

AF:

0.642

Gnomad ASJ

AF:

0.711

Gnomad EAS

AF:

0.942

Gnomad SAS

AF:

0.702

Gnomad FIN

AF:

0.762

Gnomad MID

AF:

0.775

Gnomad NFE

AF:

0.819

Gnomad OTH

AF:

0.801

GnomAD4 exome

AF:

0.669

AC:

444

AN:

664

Hom.:

176

Cov.:

AF XY:

0.686

AC XY:

269

AN XY:

392

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.900

AC:

AN:

American (AMR)

AF:

0.200

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.503

AC:

146

AN:

290

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.823

AC:

260

AN:

316

Other (OTH)

AF:

0.591

AC:

AN:

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000000229019), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.399

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.832

AC:

126509

AN:

152132

Hom.:

53592

Cov.:

AF XY:

0.822

AC XY:

61114

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.955

AC:

39678

AN:

41560

American (AMR)

AF:

0.642

AC:

9790

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.711

AC:

2467

AN:

3472

East Asian (EAS)

AF:

0.943

AC:

4876

AN:

5172

South Asian (SAS)

AF:

0.701

AC:

3381

AN:

4826

European-Finnish (FIN)

AF:

0.762

AC:

8043

AN:

10554

Middle Eastern (MID)

AF:

0.789

AC:

232

AN:

294

European-Non Finnish (NFE)

AF:

0.819

AC:

55706

AN:

67980

Other (OTH)

AF:

0.804

AC:

1697

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

993

1987

2980

3974

4967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

876

1752

2628

3504

4380

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.813

Hom.:

62614

Bravo

AF:

0.825

Asia WGS

AF:

0.845

AC:

2938

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.27

(source)

DANN

Benign

0.58

PhyloP100

-2.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over