rs287302

Variant names:

• chr2-17230419-C-A
• rs287302

Your query was ambiguous. Multiple possible variants found:

• chr2-17230419-C-A
• chr2-17230419-C-G

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 0.134 in 152,182 control chromosomes in the GnomAD database, including 3,117 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 0.13 (3117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.134 AC: 20309 AN: 152064 Hom.: 3110 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0528

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.134 AC: 20350 AN: 152182 Hom.: 3117 Cov.: 32 AF XY: 0.132 AC XY: 9843 AN XY: 74416

African (AFR) AF: 0.365 AC: 15134 AN: 41464

American (AMR) AF: 0.149 AC: 2276 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0528 AC: 183 AN: 3468

East Asian (EAS) AF: 0.128 AC: 664 AN: 5178

South Asian (SAS) AF: 0.0352 AC: 170 AN: 4828

European-Finnish (FIN) AF: 0.0208 AC: 221 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0216 AC: 1472 AN: 68020

Other (OTH) AF: 0.0993 AC: 210 AN: 2114

Alfa AF: 0.0829 Hom.: 567

Bravo AF: 0.155

Asia WGS AF: 0.0970 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.39
DANN	Benign	0.38
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs287302; hg19: chr2-17411686;