9-99096100-C-T

Variant names:

• chr9-99096100-C-T
• rs7034716

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.276 AC: 11459 AN: 41450

American (AMR) AF: 0.199 AC: 3034 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 942 AN: 3468

East Asian (EAS) AF: 0.0467 AC: 242 AN: 5184

South Asian (SAS) AF: 0.147 AC: 706 AN: 4814

European-Finnish (FIN) AF: 0.263 AC: 2774 AN: 10550

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20010 AN: 67930

Other (OTH) AF: 0.264 AC: 557 AN: 2108

Alfa AF: 0.270 Hom.: 7437

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7034716; hg19: chr9-101858382;