rs2243210

Variant names:

• chr5-132665694-G-A
• rs2243210

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 0.115 in 152,226 control chromosomes in the GnomAD database, including 1,276 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 0.11 (1276 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 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: 0.115 AC: 17443 AN: 152108 Hom.: 1273 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.115 AC: 17475 AN: 152226 Hom.: 1276 Cov.: 33 AF XY: 0.114 AC XY: 8496 AN XY: 74434

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0355

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0511

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0909 Hom.: 440

Bravo AF: 0.123

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243210; hg19: chr5-132001386;