rs7229727

Positions:

• chr18-3025466-A-G

Variant summary

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

The ENST00000516449.1(SNORA70):​n.101T>C 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 0.426 in 1,013,970 control chromosomes in the GnomAD database, including 95,575 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 0.44 (14866 hom., cov: 32)
  • Exomes 𝑓: 0.42 (80709 hom.)
• Consequence: SNORA70 ENST00000516449.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

Genes affected

SNORA70 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900407	XR_007066480.1	n.102T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNORA70	ENST00000516449.1	n.101T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66353 AN: 151876 Hom.: 14846 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.424 AC: 365462 AN: 861976 Hom.: 80709 Cov.: 12 AF XY: 0.430 AC XY: 194000 AN XY: 450988

Gnomad4 AFR exome AF: 0.466

Gnomad4 AMR exome AF: 0.437

Gnomad4 ASJ exome AF: 0.367

Gnomad4 EAS exome AF: 0.600

Gnomad4 SAS exome AF: 0.586

Gnomad4 FIN exome AF: 0.428

Gnomad4 NFE exome AF: 0.391

Gnomad4 OTH exome AF: 0.434

GnomAD4 genome AF: 0.437 AC: 66424 AN: 151994 Hom.: 14866 Cov.: 32 AF XY: 0.443 AC XY: 32940 AN XY: 74280

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.443

Alfa AF: 0.404 Hom.: 1559

Bravo AF: 0.433

Asia WGS AF: 0.610 AC: 2119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.6
DANN	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7229727; hg19: chr18-3025464;