rs2243208

Variant names:

• chr5-132665459-A-G
• rs2243208

Your query was ambiguous. Multiple possible variants found:

• chr5-132665459-A-G
• chr5-132665459-A-T

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 0.121 in 152,234 control chromosomes in the GnomAD database, including 1,277 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 0.12 (1277 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 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: 0.121 AC: 18373 AN: 152116 Hom.: 1277 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0740

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.121 AC: 18402 AN: 152234 Hom.: 1277 Cov.: 33 AF XY: 0.121 AC XY: 9008 AN XY: 74426

African (AFR) AF: 0.168 AC: 6991 AN: 41526

American (AMR) AF: 0.151 AC: 2314 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3470

East Asian (EAS) AF: 0.135 AC: 698 AN: 5178

South Asian (SAS) AF: 0.146 AC: 703 AN: 4822

European-Finnish (FIN) AF: 0.0740 AC: 786 AN: 10616

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0899 AC: 6114 AN: 68008

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.106 Hom.: 1438

Bravo AF: 0.129

Asia WGS AF: 0.143 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.68
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs2243208; hg19: chr5-132001151;