rs16925783

Variant names:

• chr9-7288704-G-A
• rs16925783

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 0.0639 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0477 AC: 1984 AN: 41552

American (AMR) AF: 0.0721 AC: 1103 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3470

East Asian (EAS) AF: 0.171 AC: 887 AN: 5178

South Asian (SAS) AF: 0.0359 AC: 173 AN: 4824

European-Finnish (FIN) AF: 0.0309 AC: 328 AN: 10602

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.0686 AC: 4664 AN: 68006

Other (OTH) AF: 0.0940 AC: 199 AN: 2116

Alfa AF: 0.0660 Hom.: 302

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs16925783; hg19: chr9-7288704;