rs16925783

chr9-7288704-G-A

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 0.0639 in 152,254 control chromosomes in the GnomAD database, including 398 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 0.064 (398 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0640 AC: 9740 AN: 152136 Hom.: 401 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0724

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.0639 AC: 9732 AN: 152254 Hom.: 398 Cov.: 32 AF XY: 0.0629 AC XY: 4680 AN XY: 74444

Gnomad4 AFR AF: 0.0477

Gnomad4 AMR AF: 0.0721

Gnomad4 ASJ AF: 0.0876

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.0359

Gnomad4 FIN AF: 0.0309

Gnomad4 NFE AF: 0.0686

Gnomad4 OTH AF: 0.0940

Alfa AF: 0.0647 Hom.: 210

Bravo AF: 0.0677

Asia WGS AF: 0.0940 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.097
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16925783; hg19: chr9-7288704;