chr9-110819079-G-A

Variant names:

• chr9-110819079-G-A
• rs509276

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 0.248 in 152,032 control chromosomes in the GnomAD database, including 5,596 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 0.25 (5596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 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: 0.248 AC: 37726 AN: 151912 Hom.: 5588 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.248 AC: 37769 AN: 152032 Hom.: 5596 Cov.: 32 AF XY: 0.244 AC XY: 18125 AN XY: 74300

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.0377

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.259

Alfa AF: 0.215 Hom.: 5063

Bravo AF: 0.256

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs509276; hg19: chr9-113581359;