chr9-90214308-G-T

Variant names:

• chr9-90214308-G-T
• rs9775226

Variant summary

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

The variant allele was found at a frequency of 0.517 in 151,356 control chromosomes in the GnomAD database, including 21,570 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 0.52 (21570 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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: 0.517 AC: 78156 AN: 151238 Hom.: 21530 Cov.: 29

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.517 AC: 78255 AN: 151356 Hom.: 21570 Cov.: 29 AF XY: 0.519 AC XY: 38343 AN XY: 73912

African (AFR) AF: 0.696 AC: 28718 AN: 41280

American (AMR) AF: 0.437 AC: 6649 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3464

East Asian (EAS) AF: 0.669 AC: 3421 AN: 5112

South Asian (SAS) AF: 0.642 AC: 3075 AN: 4788

European-Finnish (FIN) AF: 0.494 AC: 5178 AN: 10480

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.421 AC: 28476 AN: 67712

Other (OTH) AF: 0.487 AC: 1023 AN: 2100

Alfa AF: 0.490 Hom.: 2634

Bravo AF: 0.517

Asia WGS AF: 0.672 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.64
DANN	Benign	0.31
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs9775226; hg19: chr9-92976590;