rs2243208

Positions:

• chr5-132665459-A-G

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 0.121 in 152,234 control chromosomes in the GnomAD database, including 1,277 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 0.12 (1277 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.132665459A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18373 AN: 152116 Hom.: 1277 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0740

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.121 AC: 18402 AN: 152234 Hom.: 1277 Cov.: 33 AF XY: 0.121 AC XY: 9008 AN XY: 74426

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0740

Gnomad4 NFE AF: 0.0899

Gnomad4 OTH AF: 0.123

Alfa AF: 0.101 Hom.: 878

Bravo AF: 0.129

Asia WGS AF: 0.143 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243208; hg19: chr5-132001151;