2-232878399-A-G

Variant names:

• chr2-232878399-A-G
• rs778371
• NM_001394206.1:c.*2043A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394206.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNORC	NM_001394206.1	MANE Select	c.*2043A>G		3_prime_UTR	Exon 3 of 3	NP_001381135.1	A0A6M4NK13
	SNORC	NM_001346120.3		c.*2043A>G		3_prime_UTR	Exon 4 of 4	NP_001333049.2	A0A6M4NK13
	SNORC	NM_001346122.2		c.*2043A>G		3_prime_UTR	Exon 4 of 4	NP_001333051.1	A0A6M4NK13

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNORC	ENST00000331342.5	TSL:1 MANE Select	c.*2043A>G		3_prime_UTR	Exon 3 of 3	ENSP00000333208.2	Q6UX34
	SNORC	ENST00000467665.1	TSL:1	n.2477A>G		non_coding_transcript_exon	Exon 2 of 2
	SNORC	ENST00000481155.1	TSL:3	n.404-53A>G		intron	N/A

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

African (AFR) AF: 0.220 AC: 33 AN: 150

American (AMR) AF: 0.230 AC: 29 AN: 126

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 37 AN: 162

East Asian (EAS) AF: 0.128 AC: 101 AN: 788

South Asian (SAS) AF: 0.167 AC: 9 AN: 54

European-Finnish (FIN) AF: 0.255 AC: 194 AN: 762

Middle Eastern (MID) AF: 0.194 AC: 7 AN: 36

European-Non Finnish (NFE) AF: 0.247 AC: 1040 AN: 4210

Other (OTH) AF: 0.256 AC: 89 AN: 348

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

African (AFR) AF: 0.241 AC: 9978 AN: 41456

American (AMR) AF: 0.305 AC: 4662 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3468

East Asian (EAS) AF: 0.119 AC: 615 AN: 5176

South Asian (SAS) AF: 0.120 AC: 581 AN: 4824

European-Finnish (FIN) AF: 0.267 AC: 2826 AN: 10576

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19968 AN: 67970

Other (OTH) AF: 0.270 AC: 570 AN: 2110

Alfa AF: 0.279 Hom.: 8601

Bravo AF: 0.269

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		-0.11
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

Other links and lift over

dbSNP: rs778371; hg19: chr2-233743109;