rs2416666

Positions:

• chr9-99082267-G-A

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 0.118 in 152,238 control chromosomes in the GnomAD database, including 1,337 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 0.12 (1337 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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 (EAS) allele frequency at 95% confidence interval = 0.272 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: 0.118 AC: 17883 AN: 152118 Hom.: 1336 Cov.: 32

Gnomad AFR AF: 0.0308

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.117 AC: 17888 AN: 152238 Hom.: 1337 Cov.: 32 AF XY: 0.120 AC XY: 8942 AN XY: 74428

Gnomad4 AFR AF: 0.0307

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.145

Alfa AF: 0.140 Hom.: 2299

Bravo AF: 0.117

Asia WGS AF: 0.243 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2416666; hg19: chr9-101844549;