rs2675968

chr2-232871534-C-T

Variant summary

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

The NM_001394206.1(SNORC):c.73+1120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,008 control chromosomes in the GnomAD database, including 7,054 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 0.30 (7054 hom., cov: 33)
• Consequence: SNORC NM_001394206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762

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 = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNORC	NM_001394206.1	c.73+1120C>T		intron_variant		ENST00000331342.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNORC	ENST00000331342.5	c.73+1120C>T		intron_variant		1	NM_001394206.1	P1
SNORC	ENST00000409230.5	c.73+1120C>T		intron_variant		3		P1
SNORC	ENST00000409533.5	c.73+1120C>T		intron_variant		4		P1
SNORC	ENST00000695538.1	c.73+1120C>T		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45645 AN: 151890 Hom.: 7044 Cov.: 33

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.304

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.301 AC: 45684 AN: 152008 Hom.: 7054 Cov.: 33 AF XY: 0.301 AC XY: 22373 AN XY: 74288

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.299

Alfa AF: 0.302 Hom.: 1508

Bravo AF: 0.302

Asia WGS AF: 0.247 AC: 858 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	0.29
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2675968; hg19: chr2-233736244;