rs2416666

Variant names:

• chr9-99082267-G-A
• rs2416666

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 0.118 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
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.272 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: 0.118 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

African (AFR) AF: 0.0307 AC: 1277 AN: 41558

American (AMR) AF: 0.159 AC: 2437 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1473 AN: 5178

South Asian (SAS) AF: 0.231 AC: 1109 AN: 4808

European-Finnish (FIN) AF: 0.116 AC: 1234 AN: 10598

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9477 AN: 68012

Other (OTH) AF: 0.145 AC: 306 AN: 2114

Alfa AF: 0.131 Hom.: 2878

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2416666; hg19: chr9-101844549;