rs9288614

Variant names:

• chr2-225956870-C-G
• rs9288614

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 0.302 in 151,976 control chromosomes in the GnomAD database, including 9,323 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 0.30 (9323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 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: 0.302 AC: 45800 AN: 151860 Hom.: 9291 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.302 AC: 45899 AN: 151976 Hom.: 9323 Cov.: 32 AF XY: 0.303 AC XY: 22487 AN XY: 74278

African (AFR) AF: 0.578 AC: 23950 AN: 41430

American (AMR) AF: 0.164 AC: 2500 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3466

East Asian (EAS) AF: 0.342 AC: 1764 AN: 5162

South Asian (SAS) AF: 0.339 AC: 1635 AN: 4828

European-Finnish (FIN) AF: 0.237 AC: 2499 AN: 10554

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12119 AN: 67950

Other (OTH) AF: 0.241 AC: 508 AN: 2110

Alfa AF: 0.251 Hom.: 787

Bravo AF: 0.307

Asia WGS AF: 0.405 AC: 1403 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.7
DANN	Benign	0.75
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9288614; hg19: chr2-226821586;