9-117700861-A-G

Variant names:

• chr9-117700861-A-G
• rs2770150

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 0.219 in 152,144 control chromosomes in the GnomAD database, including 4,084 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 0.22 (4084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 63 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33351 AN: 152026 Hom.: 4083 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.219 AC: 33357 AN: 152144 Hom.: 4084 Cov.: 32 AF XY: 0.216 AC XY: 16075 AN XY: 74390

African (AFR) AF: 0.135 AC: 5606 AN: 41524

American (AMR) AF: 0.223 AC: 3415 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 840 AN: 3466

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5172

South Asian (SAS) AF: 0.218 AC: 1050 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2453 AN: 10588

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19096 AN: 67980

Other (OTH) AF: 0.235 AC: 495 AN: 2110

Alfa AF: 0.259 Hom.: 8579

Bravo AF: 0.216

Asia WGS AF: 0.102 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.4
DANN	Benign	0.77
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2770150; hg19: chr9-120463139;