chr22-41674272-T-C

Position:

• chr22-41674272-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNU13	NM_001003796.2	c.*661A>G		3_prime_UTR_variant	3/3	ENST00000401959.6	NP_001003796.1
SNU13	NM_005008.4	c.*661A>G		3_prime_UTR_variant	4/4		NP_004999.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNU13	ENST00000401959.6	c.*661A>G		3_prime_UTR_variant	3/3	2	NM_001003796.2	ENSP00000383949.1
SNU13	ENST00000648161.1	n.1002A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126394 AN: 152014 Hom.: 53531 Cov.: 32

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.: 0 AF XY: 0.686 AC XY: 269 AN XY: 392

Gnomad4 AFR exome AF: 0.900

Gnomad4 AMR exome AF: 0.200

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.503

Gnomad4 NFE exome AF: 0.823

Gnomad4 OTH exome AF: 0.591

GnomAD4 genome AF: 0.832 AC: 126509 AN: 152132 Hom.: 53592 Cov.: 32 AF XY: 0.822 AC XY: 61114 AN XY: 74338

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.804

Alfa AF: 0.813 Hom.: 47535

Bravo AF: 0.825

Asia WGS AF: 0.845 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.27
DANN	Benign	0.58
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

LitVar

Other links and lift over

dbSNP: rs8779; hg19: chr22-42070276;