rs2243293

Variant names:

• chr5-132684107-G-A
• rs2243293

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.409 AC: 16932 AN: 41396

American (AMR) AF: 0.563 AC: 8591 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2386 AN: 3468

East Asian (EAS) AF: 0.161 AC: 833 AN: 5168

South Asian (SAS) AF: 0.651 AC: 3131 AN: 4812

European-Finnish (FIN) AF: 0.542 AC: 5716 AN: 10546

Middle Eastern (MID) AF: 0.659 AC: 191 AN: 290

European-Non Finnish (NFE) AF: 0.747 AC: 50781 AN: 67978

Other (OTH) AF: 0.624 AC: 1317 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.14
PhyloP100		-0.24

Splicing

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

Other links and lift over

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