2-232878399-A-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001394206.1(SNORC):​c.*2043A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: SNORC NM_001394206.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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>T		3_prime_UTR	Exon 3 of 3	NP_001381135.1	A0A6M4NK13
	SNORC	NM_001346120.3		c.*2043A>T		3_prime_UTR	Exon 4 of 4	NP_001333049.2	A0A6M4NK13
	SNORC	NM_001346122.2		c.*2043A>T		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>T		3_prime_UTR	Exon 3 of 3	ENSP00000333208.2	Q6UX34
	SNORC	ENST00000467665.1	TSL:1	n.2477A>T		non_coding_transcript_exon	Exon 2 of 2
	SNORC	ENST00000481155.1	TSL:3	n.404-53A>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.55
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;