chr9-117700861-A-G

Position:

• chr9-117700861-A-G

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 0.219 in 152,144 control chromosomes in the GnomAD database, including 4,084 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 0.22 (4084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 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: 0.219 AC: 33351 AN: 152026 Hom.: 4083 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.219 AC: 33357 AN: 152144 Hom.: 4084 Cov.: 32 AF XY: 0.216 AC XY: 16075 AN XY: 74390

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.235

Alfa AF: 0.248 Hom.: 1209

Bravo AF: 0.216

Asia WGS AF: 0.102 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2770150; hg19: chr9-120463139;