rs9288520

Variant names:

• chr2-216616548-G-A
• rs9288520

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 0.144 in 152,126 control chromosomes in the GnomAD database, including 1,736 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 0.14 (1736 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 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: 0.144 AC: 21943 AN: 152006 Hom.: 1735 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.144 AC: 21958 AN: 152126 Hom.: 1736 Cov.: 32 AF XY: 0.146 AC XY: 10867 AN XY: 74370

African (AFR) AF: 0.122 AC: 5076 AN: 41508

American (AMR) AF: 0.216 AC: 3299 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3470

East Asian (EAS) AF: 0.310 AC: 1599 AN: 5156

South Asian (SAS) AF: 0.211 AC: 1014 AN: 4814

European-Finnish (FIN) AF: 0.131 AC: 1393 AN: 10594

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8748 AN: 68002

Other (OTH) AF: 0.168 AC: 354 AN: 2112

Alfa AF: 0.134 Hom.: 2595

Bravo AF: 0.150

Asia WGS AF: 0.285 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.4
DANN	Benign	0.65
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs9288520; hg19: chr2-217481271;