9-99354687-T-C

Variant names:

• chr9-99354687-T-C
• rs411102

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 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

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;