9-90801254-A-G

Variant names:

• chr9-90801254-A-G
• rs290986

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: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0200

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

Nov 02, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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;