rs9937239

Variant names:

• chr16-87073514-G-A
• rs9937239

Your query was ambiguous. Multiple possible variants found:

• chr16-87073514-G-A
• chr16-87073514-G-C

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 0.297 in 152,066 control chromosomes in the GnomAD database, including 7,046 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 0.30 (7046 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 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: 0.297 AC: 45192 AN: 151948 Hom.: 7033 Cov.: 33

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.297 AC: 45226 AN: 152066 Hom.: 7046 Cov.: 33 AF XY: 0.300 AC XY: 22321 AN XY: 74304

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.276

Alfa AF: 0.248 Hom.: 6335

Bravo AF: 0.293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9937239; hg19: chr16-87107120;