NM_001394206.1:c.73+419T>C

Variant names:

• chr2-232870833-T-C
• rs2675966
• NM_001394206.1:c.73+419T>C

Variant summary

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

The NM_001394206.1(SNORC):​c.73+419T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,090 control chromosomes in the GnomAD database, including 29,568 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 0.62 (29568 hom., cov: 32)
• Consequence: SNORC NM_001394206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 6 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNORC	NM_001394206.1	c.73+419T>C		intron_variant	Intron 1 of 2	ENST00000331342.5	NP_001381135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNORC	ENST00000331342.5	c.73+419T>C		intron_variant	Intron 1 of 2	1	NM_001394206.1	ENSP00000333208.2
SNORC	ENST00000409230.5	c.73+419T>C		intron_variant	Intron 2 of 3	3		ENSP00000386804.1
SNORC	ENST00000409533.5	c.73+419T>C		intron_variant	Intron 2 of 3	4		ENSP00000387130.1
SNORC	ENST00000695538.1	c.73+419T>C		intron_variant	Intron 2 of 3			ENSP00000511992.1

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94285 AN: 151972 Hom.: 29530 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.621 AC: 94373 AN: 152090 Hom.: 29568 Cov.: 32 AF XY: 0.623 AC XY: 46321 AN XY: 74324

African (AFR) AF: 0.656 AC: 27188 AN: 41470

American (AMR) AF: 0.649 AC: 9923 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2099 AN: 3468

East Asian (EAS) AF: 0.665 AC: 3431 AN: 5156

South Asian (SAS) AF: 0.372 AC: 1796 AN: 4828

European-Finnish (FIN) AF: 0.712 AC: 7535 AN: 10582

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40377 AN: 67980

Other (OTH) AF: 0.616 AC: 1303 AN: 2114

Alfa AF: 0.615 Hom.: 6426

Bravo AF: 0.626

Asia WGS AF: 0.492 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.82
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2675966; hg19: chr2-233735543;