9-90607502-A-G

Variant names:

• chr9-90607502-A-G
• rs7868194

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 0.474 in 152,008 control chromosomes in the GnomAD database, including 17,155 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 0.47 (17155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 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: 0.474 AC: 71975 AN: 151890 Hom.: 17146 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.474 AC: 72029 AN: 152008 Hom.: 17155 Cov.: 32 AF XY: 0.472 AC XY: 35080 AN XY: 74300

African (AFR) AF: 0.476 AC: 19713 AN: 41432

American (AMR) AF: 0.465 AC: 7106 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2008 AN: 3468

East Asian (EAS) AF: 0.348 AC: 1793 AN: 5156

South Asian (SAS) AF: 0.394 AC: 1900 AN: 4828

European-Finnish (FIN) AF: 0.486 AC: 5138 AN: 10564

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32735 AN: 67972

Other (OTH) AF: 0.480 AC: 1014 AN: 2114

Alfa AF: 0.479 Hom.: 23275

Bravo AF: 0.476

Asia WGS AF: 0.384 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.32
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs7868194; hg19: chr9-93369784;