rs9288572

Variant names:

• chr2-222097644-G-A
• rs9288572

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 0.173 in 151,968 control chromosomes in the GnomAD database, including 2,618 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 0.17 (2618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.173 AC: 26243 AN: 151850 Hom.: 2619 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.173 AC: 26255 AN: 151968 Hom.: 2618 Cov.: 32 AF XY: 0.178 AC XY: 13193 AN XY: 74288

African (AFR) AF: 0.156 AC: 6456 AN: 41488

American (AMR) AF: 0.235 AC: 3579 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 769 AN: 3468

East Asian (EAS) AF: 0.487 AC: 2505 AN: 5144

South Asian (SAS) AF: 0.191 AC: 921 AN: 4818

European-Finnish (FIN) AF: 0.165 AC: 1745 AN: 10582

Middle Eastern (MID) AF: 0.219 AC: 63 AN: 288

European-Non Finnish (NFE) AF: 0.143 AC: 9689 AN: 67920

Other (OTH) AF: 0.195 AC: 411 AN: 2108

Alfa AF: 0.154 Hom.: 298

Bravo AF: 0.179

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	11
DANN	Benign	0.72
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs9288572; hg19: chr2-222962363;