9-34050347-C-T

Variant names:

• chr9-34050347-C-T
• rs10453201
• ENST00000410327.1:n.*103C>T

Variant summary

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

The ENST00000410327.1(RN7SKP114):​n.*103C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,060 control chromosomes in the GnomAD database, including 4,019 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 0.21 (4019 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RN7SKP114 ENST00000410327.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410

Genes affected

RN7SKP114 (HGNC:45838): (RN7SK pseudogene 114)

ACMG classification

Verdict is Benign. Variant got -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 = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RN7SKP114	ENST00000410327.1	n.*103C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31836 AN: 151940 Hom.: 4019 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.239

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.209 AC: 31830 AN: 152060 Hom.: 4019 Cov.: 32 AF XY: 0.211 AC XY: 15704 AN XY: 74320

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.238

Alfa AF: 0.197 Hom.: 403

Bravo AF: 0.219

Asia WGS AF: 0.357 AC: 1239 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	2.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10453201; hg19: chr9-34050345;