rs2243293

chr5-132684107-G-A

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 0.597 in 151,948 control chromosomes in the GnomAD database, including 29,353 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 0.60 (29353 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 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: 0.597 AC: 90679 AN: 151830 Hom.: 29351 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.663

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.597 AC: 90707 AN: 151948 Hom.: 29353 Cov.: 31 AF XY: 0.586 AC XY: 43561 AN XY: 74274

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.624

Alfa AF: 0.643 Hom.: 4383

Bravo AF: 0.584

Asia WGS AF: 0.447 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.83
Dann	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243293; hg19: chr5-132019799; COSMIC: COSV51502845;