rs10117466

Positions:

• chr9-134918015-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.264 in 587,078 control chromosomes in the GnomAD database, including 23,215 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.25 (5430 hom., cov: 32)
  • Exomes 𝑓: 0.27 (17785 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0310

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 9-134918015-G-T is Benign according to our data. Variant chr9-134918015-G-T is described in ClinVar as [Benign]. Clinvar id is 1252732.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.134918015G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37977 AN: 151954 Hom.: 5431 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.00809

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.252

GnomAD4 exome AF: 0.269 AC: 117109 AN: 435006 Hom.: 17785 AF XY: 0.266 AC XY: 61001 AN XY: 229092

Gnomad4 AFR exome AF: 0.136

Gnomad4 AMR exome AF: 0.171

Gnomad4 ASJ exome AF: 0.237

Gnomad4 EAS exome AF: 0.00246

Gnomad4 SAS exome AF: 0.199

Gnomad4 FIN exome AF: 0.313

Gnomad4 NFE exome AF: 0.323

Gnomad4 OTH exome AF: 0.265

GnomAD4 genome AF: 0.250 AC: 37968 AN: 152072 Hom.: 5430 Cov.: 32 AF XY: 0.247 AC XY: 18327 AN XY: 74342

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.00792

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.248

Alfa AF: 0.288 Hom.: 2137

Bravo AF: 0.235

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 22, 2019	This variant is associated with the following publications: (PMID: 22673311, 23209787) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10117466; hg19: chr9-137809861;