rs9696070

Variant names:

• chr9-86615864-C-T
• rs9696070

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 0.417 in 151,930 control chromosomes in the GnomAD database, including 13,290 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 0.42 (13290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.445 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: 0.417 AC: 63310 AN: 151812 Hom.: 13279 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.417 AC: 63366 AN: 151930 Hom.: 13290 Cov.: 32 AF XY: 0.419 AC XY: 31083 AN XY: 74258

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.441

Alfa AF: 0.400 Hom.: 25716

Bravo AF: 0.417

Asia WGS AF: 0.459 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.82
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9696070; hg19: chr9-89230779;