rs778371

Positions:

• chr2-232878399-A-G

Variant summary

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

The NM_001394206.1(SNORC):​c.*2043A>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 0.265 in 158,708 control chromosomes in the GnomAD database, including 5,825 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 0.27 (5615 hom., cov: 33)
  • Exomes 𝑓: 0.23 (210 hom.)
• Consequence: SNORC NM_001394206.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

Genes affected

SNORC (HGNC:33763): (secondary ossification center associated regulator of chondrocyte maturation) Predicted to be involved in cartilage development. Predicted to be located in collagen-containing extracellular matrix; cytoplasm; and extracellular region. Predicted to be integral component of membrane. Predicted to be active in cell periphery. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNORC	NM_001394206.1	c.*2043A>G		3_prime_UTR_variant	3/3	ENST00000331342.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNORC	ENST00000331342.5	c.*2043A>G		3_prime_UTR_variant	3/3	1	NM_001394206.1	P1
SNORC	ENST00000467665.1	n.2477A>G		non_coding_transcript_exon_variant	2/2	1
SNORC	ENST00000481155.1	n.404-53A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40494 AN: 151954 Hom.: 5606 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.232 AC: 1539 AN: 6636 Hom.: 210 Cov.: 0 AF XY: 0.241 AC XY: 855 AN XY: 3542

Gnomad4 AFR exome AF: 0.220

Gnomad4 AMR exome AF: 0.230

Gnomad4 ASJ exome AF: 0.228

Gnomad4 EAS exome AF: 0.128

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.255

Gnomad4 NFE exome AF: 0.247

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome AF: 0.267 AC: 40528 AN: 152072 Hom.: 5615 Cov.: 33 AF XY: 0.263 AC XY: 19515 AN XY: 74330

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.270

Alfa AF: 0.279 Hom.: 775

Bravo AF: 0.269

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.41
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs778371; hg19: chr2-233743109;