rs2243300

Variant names:

• chr5-132668394-G-T
• rs2243300

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 0.065 in 152,272 control chromosomes in the GnomAD database, including 426 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 0.065 (426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 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: 0.0651 AC: 9901 AN: 152154 Hom.: 427 Cov.: 32

Gnomad AFR AF: 0.0243

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0392

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.0769

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

GnomAD4 genome AF: 0.0650 AC: 9905 AN: 152272 Hom.: 426 Cov.: 32 AF XY: 0.0661 AC XY: 4924 AN XY: 74454

Gnomad4 AFR AF: 0.0244

Gnomad4 AMR AF: 0.0936

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.0395

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0806

Gnomad4 OTH AF: 0.0751

Alfa AF: 0.0811 Hom.: 302

Bravo AF: 0.0660

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243300; hg19: chr5-132004086;