9-99096233-C-A

Position:

• chr9-99096233-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0804 in 152,210 control chromosomes in the GnomAD database, including 628 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 0.080 (628 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0979 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: 0.0804 AC: 12227 AN: 152092 Hom.: 629 Cov.: 33

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0617

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.0882

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

GnomAD4 genome AF: 0.0804 AC: 12234 AN: 152210 Hom.: 628 Cov.: 33 AF XY: 0.0803 AC XY: 5976 AN XY: 74414

Gnomad4 AFR AF: 0.0567

Gnomad4 AMR AF: 0.0616

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.0999

Gnomad4 OTH AF: 0.0873

Alfa AF: 0.0468 Hom.: 59

Bravo AF: 0.0743

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	9.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7034867; hg19: chr9-101858515;