chr9-117701869-G-A

Position:

• chr9-117701869-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 0.309 in 152,080 control chromosomes in the GnomAD database, including 8,882 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 0.31 (8882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47049 AN: 151962 Hom.: 8887 Cov.: 32

Gnomad AFR AF: 0.0917

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.309 AC: 47048 AN: 152080 Hom.: 8882 Cov.: 32 AF XY: 0.311 AC XY: 23132 AN XY: 74336

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.343

Alfa AF: 0.191 Hom.: 545

Bravo AF: 0.308

Asia WGS AF: 0.489 AC: 1700 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10759931; hg19: chr9-120464147;