9-34050347-C-T

Variant names:

• chr9-34050347-C-T
• rs10453201
• ENST00000716595.1:n.50+735C>T

Variant summary

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

The ENST00000716595.1(ENSG00000228352):​n.50+735C>T variant causes a intron 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: ENSG00000228352 ENST00000716595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 6 publications found

Genes affected

ENSG00000228352 (HGNC:58097):

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

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 = 0.568 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716595.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228352	ENST00000716595.1		n.50+735C>T		intron	N/A
	ENSG00000228352	ENST00000716596.1		n.48+735C>T		intron	N/A
	RN7SKP114	ENST00000410327.1	TSL:6	n.*103C>T		downstream_gene	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.112 AC: 4643 AN: 41496

American (AMR) AF: 0.306 AC: 4670 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 939 AN: 3470

East Asian (EAS) AF: 0.586 AC: 3026 AN: 5168

South Asian (SAS) AF: 0.241 AC: 1160 AN: 4816

European-Finnish (FIN) AF: 0.189 AC: 1999 AN: 10560

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14755 AN: 67976

Other (OTH) AF: 0.238 AC: 504 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs10453201; hg19: chr9-34050345;