chr9-109013944-G-A

Position:

• chr9-109013944-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 0.222 in 152,002 control chromosomes in the GnomAD database, including 4,494 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 (4494 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.293 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: 0.222 AC: 33714 AN: 151882 Hom.: 4490 Cov.: 33

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.222 AC: 33728 AN: 152002 Hom.: 4494 Cov.: 33 AF XY: 0.224 AC XY: 16600 AN XY: 74260

Gnomad4 AFR AF: 0.0605

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.245

Alfa AF: 0.268 Hom.: 9529

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.5
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1333344; hg19: chr9-111776224; COSMIC: COSV57702130;