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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.216 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

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0403

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0435

Gnomad4 NFE AF: 0.0825

Gnomad4 OTH AF: 0.184

Alfa AF: 0.173 Hom.: 1093

Bravo AF: 0.241

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243219; hg19: chr5-132002125;