rs2243219

Variant names:

• chr5-132666433-A-G
• rs2243219

Your query was ambiguous. Multiple possible variants found:

• chr5-132666433-A-G
• chr5-132666433-A-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 0.217 in 152,048 control chromosomes in the GnomAD database, including 6,870 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 0.22 (6870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32873 AN: 151930 Hom.: 6835 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0435

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.217 AC: 32956 AN: 152048 Hom.: 6870 Cov.: 32 AF XY: 0.212 AC XY: 15784 AN XY: 74340

African (AFR) AF: 0.546 AC: 22622 AN: 41426

American (AMR) AF: 0.156 AC: 2384 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3472

East Asian (EAS) AF: 0.0403 AC: 209 AN: 5182

South Asian (SAS) AF: 0.145 AC: 698 AN: 4822

European-Finnish (FIN) AF: 0.0435 AC: 461 AN: 10586

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0825 AC: 5605 AN: 67974

Other (OTH) AF: 0.184 AC: 389 AN: 2116

Alfa AF: 0.166 Hom.: 1615

Bravo AF: 0.241

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs2243219; hg19: chr5-132002125;