rs2243300

Variant names:

• chr5-132668394-G-T
• rs2243300

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 0.065 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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.0244 AC: 1013 AN: 41558

American (AMR) AF: 0.0936 AC: 1432 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3472

East Asian (EAS) AF: 0.0395 AC: 205 AN: 5190

South Asian (SAS) AF: 0.139 AC: 670 AN: 4822

European-Finnish (FIN) AF: 0.0436 AC: 463 AN: 10608

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0806 AC: 5480 AN: 68000

Other (OTH) AF: 0.0751 AC: 159 AN: 2116

Alfa AF: 0.0761 Hom.: 988

Bravo AF: 0.0660

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.52
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2243300; hg19: chr5-132004086;