chr2-232871534-C-T

Variant names:

• chr2-232871534-C-T
• rs2675968
• NM_001394206.1:c.73+1120C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_206895.3(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_206895.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762
• Publications: 16 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 = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_206895.3. 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.73+1120C>T		intron	N/A	NP_001381135.1
	SNORC	NM_001346120.3		c.73+1120C>T		intron	N/A	NP_001333049.2
	SNORC	NM_001346122.2		c.73+1120C>T		intron	N/A	NP_001333051.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNORC	ENST00000331342.5	TSL:1 MANE Select	c.73+1120C>T		intron	N/A	ENSP00000333208.2
	SNORC	ENST00000409230.5	TSL:3	c.73+1120C>T		intron	N/A	ENSP00000386804.1
	SNORC	ENST00000409533.5	TSL:4	c.73+1120C>T		intron	N/A	ENSP00000387130.1

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

African (AFR) AF: 0.252 AC: 10449 AN: 41480

American (AMR) AF: 0.354 AC: 5408 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1810 AN: 5136

South Asian (SAS) AF: 0.205 AC: 986 AN: 4814

European-Finnish (FIN) AF: 0.344 AC: 3639 AN: 10582

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21318 AN: 67922

Other (OTH) AF: 0.299 AC: 630 AN: 2110

Alfa AF: 0.306 Hom.: 13026

Bravo AF: 0.302

Asia WGS AF: 0.247 AC: 858 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	0.29
DANN	Benign	0.59
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2675968; hg19: chr2-233736244;