rs9937239

Positions:

• 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.87073514G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;