9-99096100-C-T

Position:

• chr9-99096100-C-T

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 0.263 in 151,988 control chromosomes in the GnomAD database, including 5,520 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 (5520 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.99096100C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39961 AN: 151870 Hom.: 5501 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0464

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.263 AC: 40020 AN: 151988 Hom.: 5520 Cov.: 33 AF XY: 0.257 AC XY: 19069 AN XY: 74294

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0467

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.264

Alfa AF: 0.269 Hom.: 6784

Bravo AF: 0.258

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.42
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7034716; hg19: chr9-101858382;