9-99354687-T-C

Position:

• chr9-99354687-T-C

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 0.819 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.835

Alfa AF: 0.865 Hom.: 32035

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs411102; hg19: chr9-102116969;