9-116419515-G-A

Position:

• chr9-116419515-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 0.265 in 152,086 control chromosomes in the GnomAD database, including 5,492 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 0.26 (5492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 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: 0.265 AC: 40273 AN: 151968 Hom.: 5492 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.265 AC: 40289 AN: 152086 Hom.: 5492 Cov.: 32 AF XY: 0.261 AC XY: 19409 AN XY: 74358

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.284

Alfa AF: 0.284 Hom.: 7009

Bravo AF: 0.261

Asia WGS AF: 0.150 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.16
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17303101; hg19: chr9-119181794; COSMIC: COSV62538672;