rs2282288

Variant names:

• chr1-177923417-G-A
• rs2282288

Your query was ambiguous. Multiple possible variants found:

• chr1-177923417-G-A
• chr1-177923417-G-T

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 0.323 in 151,954 control chromosomes in the GnomAD database, including 8,235 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 0.32 (8235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 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: 0.323 AC: 49081 AN: 151836 Hom.: 8223 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.323 AC: 49119 AN: 151954 Hom.: 8235 Cov.: 32 AF XY: 0.320 AC XY: 23780 AN XY: 74248

African (AFR) AF: 0.257 AC: 10622 AN: 41404

American (AMR) AF: 0.313 AC: 4781 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1402 AN: 3464

East Asian (EAS) AF: 0.243 AC: 1258 AN: 5172

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4810

European-Finnish (FIN) AF: 0.332 AC: 3494 AN: 10536

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.363 AC: 24686 AN: 67968

Other (OTH) AF: 0.348 AC: 733 AN: 2108

Alfa AF: 0.346 Hom.: 3173

Bravo AF: 0.319

Asia WGS AF: 0.363 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.60
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2282288; hg19: chr1-177892552;