rs2243211

chr5-132665730-C-Achr5-132665730-C-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 0.0919 in 152,242 control chromosomes in the GnomAD database, including 742 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 0.092 (742 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0918 AC: 13972 AN: 152124 Hom.: 742 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0770

Gnomad OTH AF: 0.0999

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

GnomAD4 genome AF: 0.0919 AC: 13987 AN: 152242 Hom.: 742 Cov.: 33 AF XY: 0.0921 AC XY: 6852 AN XY: 74424

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0355

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0512

Gnomad4 NFE AF: 0.0771

Gnomad4 OTH AF: 0.0979

Alfa AF: 0.0495 Hom.: 59

Bravo AF: 0.0964

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.65
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243211; hg19: chr5-132001422;