rs290986

Positions:

• chr9-90801254-A-G
• chr9-90801254-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.189 in 152,170 control chromosomes in the GnomAD database, including 3,019 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (3019 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 9-90801254-A-G is Benign according to our data. Variant chr9-90801254-A-G is described in ClinVar as [Benign]. Clinvar id is 1275221.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.90801254A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28775 AN: 152052 Hom.: 3023 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.192

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.189 AC: 28777 AN: 152170 Hom.: 3019 Cov.: 33 AF XY: 0.192 AC XY: 14299 AN XY: 74376

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.194

Alfa AF: 0.192 Hom.: 5051

Bravo AF: 0.185

Asia WGS AF: 0.309 AC: 1079 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 02, 2020

This variant is associated with the following publications: (PMID: 25526461) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs290986; hg19: chr9-93563536;