rs2243228

Variant names:

• chr5-132668671-A-C
• rs2243228

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 0.109 in 152,192 control chromosomes in the GnomAD database, including 1,078 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 0.11 (1078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 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: 0.109 AC: 16576 AN: 152074 Hom.: 1077 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0511

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.109 AC: 16607 AN: 152192 Hom.: 1078 Cov.: 32 AF XY: 0.108 AC XY: 8059 AN XY: 74416

African (AFR) AF: 0.164 AC: 6810 AN: 41524

American (AMR) AF: 0.119 AC: 1820 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3470

East Asian (EAS) AF: 0.0516 AC: 267 AN: 5172

South Asian (SAS) AF: 0.145 AC: 701 AN: 4818

European-Finnish (FIN) AF: 0.0448 AC: 475 AN: 10604

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0845 AC: 5748 AN: 67996

Other (OTH) AF: 0.107 AC: 225 AN: 2108

Alfa AF: 0.109 Hom.: 321

Bravo AF: 0.117

Asia WGS AF: 0.110 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.73
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs2243228; hg19: chr5-132004363;