chr9-99354687-T-C

Variant names:

• chr9-99354687-T-C
• rs411102

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 0.819 in 152,160 control chromosomes in the GnomAD database, including 51,824 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 0.82 (51824 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.884 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: 0.819 AC: 124571 AN: 152044 Hom.: 51818 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.819 AC: 124612 AN: 152160 Hom.: 51824 Cov.: 32 AF XY: 0.824 AC XY: 61296 AN XY: 74406

African (AFR) AF: 0.655 AC: 27158 AN: 41484

American (AMR) AF: 0.896 AC: 13707 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3012 AN: 3472

East Asian (EAS) AF: 0.873 AC: 4526 AN: 5186

South Asian (SAS) AF: 0.881 AC: 4256 AN: 4830

European-Finnish (FIN) AF: 0.905 AC: 9563 AN: 10568

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.877 AC: 59626 AN: 68010

Other (OTH) AF: 0.835 AC: 1763 AN: 2112

Alfa AF: 0.862 Hom.: 42849

Bravo AF: 0.811

Asia WGS AF: 0.875 AC: 3035 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.72
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs411102; hg19: chr9-102116969;