rs7022486

Positions:

• chr9-75409523-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0394 in 152,220 control chromosomes in the GnomAD database, including 237 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 0.039 (237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0929 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0391 AC: 5952 AN: 152102 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0419

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0579

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.00735

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00910

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0394 AC: 5997 AN: 152220 Hom.: 237 Cov.: 32 AF XY: 0.0404 AC XY: 3004 AN XY: 74432

Gnomad4 AFR AF: 0.0954

Gnomad4 AMR AF: 0.0418

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.0582

Gnomad4 SAS AF: 0.0550

Gnomad4 FIN AF: 0.00735

Gnomad4 NFE AF: 0.00910

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0155 Hom.: 54

Bravo AF: 0.0429

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7022486; hg19: chr9-78024439;