Genetic Variant SNORC:n.2477A>G (chr2-232878399-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000467665.1(SNORC):n.2477A>G variant causes a non coding transcript exon 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
ENST00000467665.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.114

Publications

22 publications found

Variant links:

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]

SNORC links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNORC	NM_001394206.1 link	c.*2043A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000331342.5	NP_001381135.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SNORC	ENST00000467665.1 link	n.2477A>G	non_coding_transcript_exon_variant	Exon 2 of 2	1
SNORC	ENST00000331342.5 link	c.*2043A>G	3_prime_UTR_variant	Exon 3 of 3	1	NM_001394206.1	ENSP00000333208.2	Q6UX34
SNORC	ENST00000481155.1 link	n.404-53A>G	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40494

AN:

151954

Hom.:

5606

Cov.:

show subpopulations

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.:

AF XY:

0.241

AC XY:

855

AN XY:

3542

show subpopulations

African (AFR)

AF:

0.220

AC:

AN:

150

American (AMR)

AF:

0.230

AC:

AN:

126

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

AN:

162

East Asian (EAS)

AF:

0.128

AC:

101

AN:

788

South Asian (SAS)

AF:

0.167

AC:

AN:

European-Finnish (FIN)

AF:

0.255

AC:

194

AN:

762

Middle Eastern (MID)

AF:

0.194

AC:

AN:

European-Non Finnish (NFE)

AF:

0.247

AC:

1040

AN:

4210

Other (OTH)

AF:

0.256

AC:

AN:

348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

109

164

218

273

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.267

AC:

40528

AN:

152072

Hom.:

5615

Cov.:

AF XY:

0.263

AC XY:

19515

AN XY:

74330

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.294

AC:

19968

AN:

67970

Other (OTH)

AF:

0.270

AC:

570

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1571

3142

4714

6285

7856

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.8

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over